Phylogenetic Modeling of Heterogeneous Gene-Expression Microarray Data from Cancerous Specimens

Abstract

The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes; and allows data pooling as well as comparability of intra- and interplatforms. Parsimony phylogenetic analysis of the polarized values produces a multidimensional classification of specimens into clades that reveal shared derived gene expressions (the synapomorphies); provides better assessment of ontogenic pathways and phyletic relatedness of specimens; efficiently utilizes dichotomously expressed genes; produces highly predictive class recognition; illustrates gene linkage and multiple developmental pathways; provides higher concordance between gene lists; and projects the direction of change among specimens. Further implication of this phylogenetic approach is that it may transform microarray into diagnostic, prognostic, and predictive tool.

Introduction

Gene microarray has been employed in studying comparative gene expression in cancer, genetic disorders, infections, drug response and interactions, as well as other biological processes (Quackenbush, 2006), and its data used to generate cancer taxonomy (Bittner et al., 2000; Golub, et al., 1999; Lossos and Morgensztern, 2006), diagnosis, prognosis (Beer, et al., 2002), subtyping/class discovery (Alizadeh, et al., 2000; Beer et al., 2002), and biomarker detection (Lossos and Morgensztern, 2006). However, after more than a decade since its introduction and subsequent wide usage, microarray gene expression is still facing a number of problems that are limiting its usefulness and potential (Harrison et al., 2007; Millenaar et al., 2006; Wang, et al., 2005). There are the problems of reproducibility of measurements between runs, instruments, or laboratories; the inability to perform intra- and interplatform comparability, pooling, and insufficient concordance of gene lists. Furthermore, there is the lack of an optimal bioinformatic tool to model the heterogeneity of gene expression of cancerous specimens, and due to the multiphasic nature of cancer, statistically significant gene expressions are not necessarily biologically meaningful during all phases of cancer. Current analytical paradigms such as phenetic clustering and maximum likelihood (including Bayesian) have not resolved these issues (Abu-Asab et al., 2008), and there is a total lack of an analytical paradigm that can transform microarray data into a multi-dimensional bioinformatic tool useful for a clinical setting.

Cancer incipience, progression, and maintenance are all evolutionary processes at the cellular and tissue levels; they mirror similar evolutionary processes at the population levels in that they all involve genetic modifications within an individual, selective pressure, and clonal propagation. Tumors derived from the same primary tumor become diverse and contain heterogeneous patterns of gene expression after a brief time of divergence. Data heterogeneity points out the existence of several phenomena: high genomic diversity in diseased specimens, high mutation rate, and possibly multiple pathways of disease development. To efficiently and accurately model these phenomena, biologically compatible methods of analysis should be used.

In an attempt to resolve some of the above listed problems through biologically compatible methodology and broaden the bioinformatic potential of the microarray technology, we introduce a parsimony phylogenetic approach for microarray data analysis that is based on outgroup comparison (a.k.a. polarity assessment) and maximum parsimony. This approach is a double-algorithmic procedure where the data values are first polarized into derived or ancestral depending on whether they fall within the range of the outgroup, which is usually composed of normal healthy specimens, then the polarized data is processed with a maximum parsimony algorithm. Maximum parsimony produces a phylo-genetic classification of the specimens that recognizes monophyletic classes (clades) that are delimited by shared derived gene expressions (the synapomorphies); it achieves that by finding the phylogenetic tree with the minimum steps to construct.

Biologically meaningful modeling and interpretation of the data, and better correlation with clinical characteristics, diagnosis, and outcomes are highly desired criteria in an analytical tool (Allison et al., 2006; Beer, et al., 2002; Bittner, et al., 2000; Golub, et al., 1999). Clustering specimens into unidimensional classification of discernable entities on the basis of overall quantitative gene expression similarities has some serious drawbacks (Allison et al., 2006; Lyons-Weiler et al., 2004), and appears to be incongruent with the nature of disease development (Abu-Asab, et al., 2006; 2008). In this report, we are demonstrating that the use of parsimony phylogenetic analysis of microarray data resolves the issues of gene-ranking discrepancies, improves interplatform concordance, makes possible intra- and interplatform comparability, eliminates biases in the gene linkage criteria, and casts gene expression profiles into a biologically relevant and predictive model of class discovery.

A superior classification is one that summarizes maximum knowledge about its specimens, reflects their true ontogenic relationships to one another, and offers predictivity (Farris, 1979; Golub, et al., 1999). The latter would especially be significant when the classification is applied in a clinical setting for diagnosis, prognosis, or posttreatment evaluation. We are utilizing parsimony phylogenetics because of its inherent ability to produce a robust classification of relationships—class discovery; and its forecasting power to reveal the characters of a specimen when its place in the classification is established—class prediction (Albert, 2005b). Parsimony models the heterogeneity of cancerous microarray data without any a priori assumptions (Goloboff and Pol, 2005; Siddall, 1998; Stefankovic and Vigoda, 2007). Additionally, a phylogenetic approach elucidates the direction of change among specimens that leads to their molecular and cellular diversity: the presence of one or more developmental pathway (Abu-Asab et al., 2008), and novel expressions that are involved in the progression and maintenance of the disease.

A strict parsimony phylogenetic analysis uses only shared derived values, synapomorphies, to delimit a natural group of specimens within a clade (Wiley and Siegel-Causey, 1991). Shared derived values of a gene among several specimens constitute a synapomorphy; therefore, only a synapomorphy is indicative of their relatedness. Because synapomorphies define clades at various grouping levels, a parsimonious phylogenetic classification reflects hierarchical shared developmental pathways among a group of specimens and may reveal the presence of subclasses with each having its own uniquely derived gene expression synapomorphies. In biological and clinical senses, class discovery and prediction should be based on shared derived gene expressions (i.e., synapomorphies). For example, a cancer class (a clade in phylogenetic terminology) is delimited by one or more synapomorphies, and a cancerous specimen will be placed in a class only if it shares the same synapomorphies with the members of the clade.

In this study, we are describing a double-algorithmic analytical method of microarray gene-expression data based on polarity assessment algorithm, UNIPAL (Abu-Asab, et al., 2006) where the polarized values can be used by a parsimony algorithm, MIX (Felsenstein, 1989) to produce a phylogenetic classification of specimens. This approach brings in a systematic solution to class discovery through phylogenetic classification whereby every class is delimited by shared derived gene expressions—i.e., synapomorphies-delimited clades. Because such a classification reflects the shared aberrations of gene expressions of the specimens, we expect it to have a biological and clinical relevance, and to advance targeted treatments of disease.

Materials and Methods

Gene expression datasets

In order to demonstrate the applicability of parsimony phylogenetics to microarray gene expression data, and test the results of interplatform concordance and comparability, we downloaded three publicly available datasets of gene expression comparative studies, GDS484 (Hoffman et al., 2004), GDS533 (Quade et al., 2004), and GDS1210 (Hippo et al., 2002), from NCBI’s Gene Expression Omnibus (http://www. ncbi.nlm.nih.gov/geo/). The GDS484 was conducted on GPL96 (Affymetrix GeneChip Human Genome U133 Array Set HG-U133A), and the other two studies on GPL80 (Affymetrix GeneChip Human Full Length Array HuGeneFL). The GDS484 was comprised of normal myometrium (n = 5) and uterine leiomyomas (n = 5) obtained from fibroid afflicted patients. The GDS533 study encompassed normal myometrium (n = 4), benign uterine leiomyoma (n = 7), as well as malignant uterine (n = 9) and extrauterine (n = 4) leiomyosarcoma specimens. The GDS1210 study included expression profiling of 22 primary advanced gastric cancer tissues and 8 normal specimens.

Polarity assessment and parsimony analysis

Polarity assessment through outgroup comparison does not use comparison of means and folds but rather it converts the continuous values into discontinuous ones through the assessment of each gene’s values against that of the normals’ range and produces a matrix of polarized values (0s and 1s). Our polarity assessment program, UNIPAL, compares independently each gene’s value of experimental specimens against its corresponding range within the outgroup, and scores each as either derived (1) or ancestral (0), so the matrix of gene expression values is transformed into a matrix of polarized scores (0s and 1s).

We used all the expression data points of all specimens in the analysis without any a priori selection of only a specific cluster of data. For polarity assessment (apomorphic [or derived] versus plesiomorphic [or ancestral]), data was polarized with our customized algorithm (UNIPAL) that recognized derived values of each gene when compared with the outgroups (Abu-Asab et al., 2006). Outgroups here were composed of normal healthy specimens only. Ideally, the outgroup should be large enough to encompass the maximum variation within normal healthy population. UNIPAL is freely available for noncommercial use from the authors.

The phylogenetic analysis was carried out with MIX, the maximum parsimony program of PHYLIP ver. 3.57c (Felsenstein, 1989), to produce separate parsimony phylogenetic analyses for each dataset, and the inclusive matrix of the two sets (GDS533 and GDS1210), which included all their specimens. MIX was run in randomized and nonrandomized inputs, and no significant differences were observed between the two options.

Phylogenetic trees were drawn using TreeView (Page, 1996).

Interplatform concordance and comparability

To test interplatform concordance when analyzed parsimoniously, we compared the synapomorphies of the two uterine leiomyoma datasets, GDS484 and GDS533, and recorded the percentage of concordance.

To test interplatform comparability (i.e., whether datasets can be pooled together for a parsimony analysis), we combined the polarized matrices of the two identical platform datasets, GDS533 and GDS1210, processed the combined matrix by MIX, and compared the result to their separate cladograms.

Results

The implications of a parsimonious analysis of the gene expression data are realized at several aspects: the recognition and utilization of partially asynchronous genes and dichotomously expressed asynchronous genes; the implications of outgroup selection and its effect on significant gene listing, better interplatform concordance and comparability, as well as the practical usefulness of the multidimensional cladograms.

Dichotomously expressed asynchronous (DEA) genes

Our analysis identified a specific punctuated pattern of gene expression that seemed to occur only in a set of specimens where a gene’s expression values were around the normals’ distribution (over and underexpressed), but did not overlap with it (Table 1–Table 7). This pattern has been only recognized once in the literature but was not named (Lyons-Weiler et al., 2004); we termed this phenomenon dichotomous asynchronicity to reflect its two-tailed distribution and deviation from the normal expression range.

TABLE 1.

SYNAPOMORPHIES DEFINING A CLADE OF LEIOMYOMA AND LEIOMYOSARCOMA SPECIMENS IN COMPARISON TO NORMAL SPECIMENS (GDS533)

A. Overexpressed synapomorphic genes:
D00596	TYMS thymidylate synthetase	OE[1, 2]
B. Underexpressed synapomorphic genes:
L19871	ATF3 activating transcription factor 3	UE[1, 2]
U62015	CYR61 cysteine-rich, angiogenic inducer, 61	UE[1, 2]
X68277	DUSP1 dual specificity phosphatase 1	UE[1, 2]
V01512	FOS v-fos FBJ murine osteosarcoma viral oncogene homolog	UE[1], NS [2]
L49169	FOSB FBJ murine osteosarcoma viral oncogene homolog B	NS[1], UE[2]
J04111	JUN v-jun sarcoma virus 17 oncogene homolog (avian)	UE[1, 2]
Y00503	KRT19 keratin 19	UE[1], NS [2]
U24488	TNXB tenascin XB	UE[1], UE,OE[2]
C. Dichotomously-expressed synapomorphic genes:
M31994	ALDH1A1 aldehyde dehydrogenase 1 family, member A1	UE[1], NS[2]
X05409	ALDH2 aldehyde dehydrogenase 2 family (mitochondrial)	NS[1, 2]
D25304	ARHGEF6 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	NS[1, 2]
K03430	C1QB complement component 1, q subcomponent, B chain	NS[1], OE[2]
U60521	CASP9 caspase 9, apoptosis-related cysteine peptidase	NS[1, 2]
M73720	CPA3 carboxypeptidase A3 (mast cell)	NS[1, 2]
HG2663-HT2759_at	Cpg-Enriched DNA, Clone S19 (HG3995-HT4265)	NS[1, 2]
M14676	FYN oncogene related to SRC, FGR, YES	NS[1, 2]
M34677	F8A1 coagulation factor VIII-associated (intronic transcript) 1	OE,UE[2]
U60061	FEZ2 fasciculation and elongation protein zeta 2 (zygin II)	NS[1, 2]
U86529	GSTZ1 glutathione transferase zeta 1 (maleylacetoacetate isomerase)	NS[1, 2]
HG358-HT358_at	Homeotic Protein 7, Notch Group (HG358-HT358)	NS[2]
AB002365	KIAA0367 BCH motif-containing molecule at the carboxyl terminal region 1	NS[1], OE,UE[2]
U37283	MFAP5 microfibrillar associated protein 5	NS[1, 2]
HG406-HT406_at	MFI2 antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	NS[1, 2]
M55593	MMP2 matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	NS[1], OE,UE[2]
M76732	MSX1 msh homeobox homolog 1	NS[1, 2]
L48513	PON2 paraoxonase 2	NS[1, 2]
U77594	RARRES2 retinoic acid receptor responder (tazarotene induced) 2	NS[1, 2]
M11433	RBP1 retinol binding protein 1	NS[1, 2]
L03411	RDBP RD RNA binding protein	NS[1], OE[2]
Z29083	TPBG trophoblast glycoprotein	NS[1, 2]
S73591	TXNIP thioredoxin interacting protein	NS[1, 2]

Synapomorphies include: OE gene, 8 UE genes, and 23 DE genes. Last column reports the status of the synapomorphies as described by [1] Hoffman et al. (2004) and [2] Quade et al. (2004) in their significant genes’ lists. DE = dichotomously-expressed; NS = not significant; OE = overexpressed; UN = underexpressed.

TABLE 7.

INTERPLATFORM CONCORDANCE

GDS533	GDS484
A. Overexpressed synapomorphic genes:
a. Identical Synapomorphies
DDB2	DDB2
FUT8	FUT8
MEST	MEST
TMSL8	TMSL8
TYMS	TYMS
b. Homologous synapomorphies
CACNB3	CACNA1C
COL5A2	COL4A5
KIAA0367	KIAA0101
PRKAR1B	PRKACB
B. Underexpressed synapomorphic genes:
a. Identical synapomorphies
ALDH1A1	ALDH1A1
ALDH2	ALDH2
ATF3	ATF3
CEBPD	CEBPD
CXADR	CXADR
CYR61	CYR61
DUSP1	DUSP1
FOS	FOS
HRASLS3	HRASLS3
IER2	IER2
JUN	JUN
KRT19	KRT19
RARRES2	RARRES2
TACSTD2	TACSTD2
TNXB	TNXB
VIL2	VIL2
b. Homologous synapomorphies
CASP9	CASP4
CYBA	CYB5R1
FOSB	FOS
JUNB	JUN
PPP4C	PPP1R10
SLC20A1	SLC18A2
THBS1	THBD
WDR43	WDR37
C. Dichotomously expressed synapomorphic genes:
a. Identical synapomorphies
CTSB	CTSB
b. Homologous synapomorphies
ARL4D	ARL4C
FOXO1A	FOXJ3
GNB3	GNB1L
ITGA6	ITGA2B
ITGA9	ITGA2B
KCNK1	KCNJ5
MFAP5	MFAP4
PSMC3	PSMC2
SELP	SELL
TXNIP	TXNDC13
ZNF43	ZNF259P

A list of overlapping identical (22) and homologous (23) synapomorphic genes in leiomyoma specimens of GDS484 and GDS533. These include: 9 OE, 24 UE, and 12 DE.

Although t-statistic and fold-change may dismiss these asynchronous genes from the list of differentially expressed genes, or misrepresent their significance (Lyons-Weiler et al., 2004), an outgroup polarity assessment will assess each value as derived and let the parsimony algorithm reveal its significance in relation to the rest of the genes. A parsimony phylogenetic algorithm uses the polarized values of all genes to produce the most parsimonious classification, the one with the lowest number of reversals and parallelisms (i.e., minimizes multiple origins of expression states in hypothesizing the relationships among the specimens) (Albert, 2005a; Felsenstein, 2004).

Through polarity assessment a large number of DEA genes were recognized. All these genes had their expression values above and below that of the normal specimens’ range, that is, derived in relation to outgroups thus pointing out the heterogeneity that exists among specimens. DEA genes were found in all the three datasets studied here (Table 1–Table 7), and were included within all the analyses.

Most parsimonious cladograms

Parsimony analysis produced one most parsimonious cladogram (having the least number of steps in constructing a classification of specimens) for the uterine GDS533 dataset (Fig. 1). The topology of the tree showed one large inclusive clade that encompassed all of the leiomyomas and leiomyosarcomas delimited by 32 synapomorphies (Table 1), a terminal clade with nine sarcoma specimens, middle sarcoma clade with four specimens, five small basal leiomyoma clades in tandem arrangement, followed by four basal normal clades.

FIG. 1.

A cladogram of a parsimony phylogenetic analysis of microarray gene-expression data representing normal myometrium (n = 4), leiomyoma (n = 7), leiomyosarcoma (n = 9), and extrauterine leiomyosarcoma (n = 4) specimens. The leiomyomas and leiomyosarcomas form a clade defined by 32 synapomorphies (Table 1). The leiomyosarcoma specimens form a terminal clade that is circumscribed by 20 synapomorphies (Table 3). Asterisk (*) denotes extrauterine leiomyosarcomas.

The cladogram in Figure 1 showed that the leiomyoma specimens did not form a natural group by themselves—they did not form their own clade separating them from the leiomyosarcomas, and there were no synapomorphies circumscribing them as a clade when the ingroup was composed of leiomyoma and leiomyosarcoma and the outgroup composed of the normals. However, the leiomyomas shared 146 synapomorphies distinguishing them from the normals (Table 2).

TABLE 2.

SYNAPOMORPHIES OF LEIOMYOMA SPECIMENS IN COMPARISON TO NORMAL SPECIMENS (GDS533)

A. Overexpressed synapomorphic genes:
D16469	ATP6AP1 ATPase, H+ transporting, lysosomal accessory protein 1	NS[1, 2]
U07139	CACNB3 calcium channel, voltage-dependent, beta 3 subunit	NS[1], OE[2]
M11718	COL5A2 collagen, type V, alpha 2	NS[1, 2]
U18300	DDB2 damage-specific DNA binding protein 2, 48 kDa	NS[1, 2]
D38550	E2F3 E2F transcription factor 3	NS[1, 2]
M34677	F8A1 coagulation factor VIII-associated (intronic transcript) 1	NS[1, 2]
D89289	FUT8 fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	NS[1, 2]
D86962	GRB10 growth factor receptor-bound protein 10	NS[1, 2]
M32053	H19, imprinted maternally expressed untranslated mRNA	NS[1, 2]
U07664	HLXB9 homeobox HB9	OE[1, 2]
D87452	IHPK1 inositol hexaphosphate kinase 1	NS[1, 2]
U51336	ITPK1 inositol 1,3,4-triphosphate 5/6 kinase	NS[1, 2]
ABA002365	KIAA0367	NS[1], OE[2]
D78611	MEST mesoderm specific transcript homolog (mouse)	OE[1], NS[2]
U19718	MFAP2 microfibrillar-associated protein 2	NS[1, 2]
M55593	MMP2 matrix metallopeptidase 2 (gelatinase A, 72 kDa gelatinase, 72kDa type IV collagenase)	OE[1, 2]
U79247	PCDH11X protocadherin 11 X-linked	NS[1, 2]
L24559	POLA2 polymerase (DNA directed), alpha 2 (70 kDa subunit)	NS[1, 2]
M65066	PRKAR1B protein kinase, cAMP-dependent, regulatory, type I, beta	NS[1, 2]
D14694	PTDSS1 phosphatidylserine synthase 1	NS[1, 2]
U24186	RPA4 replication protein A4, 34 kDa	NS[1, 2]
U85658	TFAP2C transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	NS[1, 2]
D82345	TMSL8 thymosin-like 8	NS[1, 2]
D85376	TRHR thyrotropin-releasing hormone receptor	NS[1, 2]
D00596	TYMS* thymidylate synthetase	OE[1, 2]
B. Underexpressed synapomorphic genes:
X0330	ADH1B alcohol dehydrogenase IB (class I), beta polypeptide	NS[1, 2]
M31994	ALDH1A1* aldehyde dehydrogenaes 1 family, member A1	UE[1], NS[2]
X05409	ALDH2* aldehyde dehydrogenase 2 family (mitochondrial)	NS[1, 2]
L19871	ATF3* activating transcription factor 3	UE[1, 2]
U60521	CASP9 caspase 9, apoptosis-related cysteine peptidase	NS[1, 2]
D49372	CCL11 chemokine (C—C motif) ligand 11	NS[1, 2]
X05323	CD200 molecule	NS[1, 2]
M83667	CEBPD CCAAT/enhancer binding protein (C/EBP), delta	NS[1, 2]
U90716	CXADR coxsackie virus and adenovirus receptor	NS[1, 2]
M21186	CYBA cytochrome b-245, alpha polypeptide	NS[1, 2]
U62015	CYR61* cysteine-rich, angiogenic inducer, 61	UE[1, 2]
Z22865	DPT dermatopontin	NS[1, 2]
X56807	DSC2 desmocollin 2	NS[1, 2]
X68277	DUSP1* dual specificity phosphatase 1	UE[1, 2]
V01512	FOS* v-fos FBJ murine osteosarcoma viral oncogene homolog	UE[1], NS[2]
L49169	FOSB FBJ murine osteosarcoma viral oncogene homolog B	NS[1], UE[2]
L11238	GP5 glycoprotein V (platelet)	NS[1, 2]
M36284	GYPC glycophorin C (Gerbich blood group)	NS[1, 2]
M60750	HIST1H2BG histone cluster 1, H2bg	NS[1, 2]
X79200	Homo spaiens mRNA for SYT-SSX protein	NS[1, 2]
X92814	HRASLS3 HRAS-like suppressor 3	NS[1, 2]
M62831	IER2 immediate early response 2	NS[1, 2]
J04111	JUN* v-jun sarcoma virus 17 oncogene homolog (avian)	UE[1, 2]
Y00503	KRT19* keratin 19	NS[1, 2]
X89430	MECP2 methyl CpG binding protein 2 (Rett syndrome)	NS[1, 2]
U46499	MGST1 microsomal glutathione S-transferase 1	NS[1, 2]
M93221	MRC1 mannose receptor, C type 1	NS[1, 2]
M76732	MSX1* msh homeobox homolog 1 (Drosophila)	NS[1, 2]
S71824	NCAM1 neural cell adhesion molecule 1	OE[1], NS[2]
X70218	PPP4C protein phosphatase 4	NS[1, 2]
U02680	PTK9 protein tyrosine kinase 9	NS[1, 2]
U79291	PTPN11 protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)	NS[1, 2]
U77594	RARRES2* retinoic acid receptor responder (tazarotene induced) 2	NS[1, 2]
M11433, X07438	RBP1* retinol binding protein 1, cellular	NS[1, 2]
L20859	SLC20A1 solute carrier family 20 (phosphate transporter), member 1	NS[1, 2]
M97935	STAT1 signal transducer and activator of transcription 1, 91kDa	NS[1, 2]
J04152	TACSTD2 tumor-associated calcium signal transducer 2	NS[1, 2]
X14787	THBS1 thrombospondin 1	NS[1, 2]
U24488	TNXB* tenascin XB	UE[1, 2]
Z29083	TPBG* trophoblast glycoprotein	NS[1, 2]
X51521	VIL2 villin 2 (ezrin)	UE[1], NS[2]
D87716	WDR43 WD repeat domain 43	NS[1, 2]
C. Dichotomously-expressed synapomorphic genes:
ABCB1; ADRM1; AIM1; ALDH1A3; AMDD; ARHGEF6; ARL4D; ATP5B; Atp8a2; C1QB; CA9; CALM2; CTSB; CCRL2; CD52; CD99; CPA3; DPYD; DSG2; Emx2; FEZ2; FLNA; FOXO1A; FYN; GAPDH; GNB3; GSTZ1; H1F0; H2-ALPHA; HBG2; Ubx, Notch1; Hox5.4; HTR2C; ICA1; IGF2; INSR; ITGA6; ITGA9; KCNK1; KIAA0152; MAP1D; MATK; MBP; MDM4; MFAP5; MFI2 antigen p97; MLH1; MPZ; NDUFS1; NELL2; NNAT; NOS3; NR4A1; OASL; ODC1; OLFM1; PKN2; PON2; PRMT2; PSMC3; PTR2; RANBP2; RBMX; RDBP; RHOG; SAFB2; SCRIB; SELFP; SERPINF1; SMS; SPOCK2; ST3GAL1; THRA; TNXB; TTLL4; TXNIP; UPK2; XA; ZNF43

These comprise: 25 OE genes, 42 UE genes, and 79 DE genes.

Asterisk (*) indicates a synapomorphy for leiomyosarcoma as well. Last column reports the status of the synapomorphies as described by [1] Hoffman et al. (2004) and [2] Quade et al. (2004) in their significant genes lists.

The 13 leiomyosarcoma specimens separated into a large terminal clade that was delimited by 20 synapomorphies in comparison with an outgroup composed of leiomyoma and normal specimens (Table 3), and 29 synapomorphies derived in relation to leiomyomas only as an outgroup (Table 4). Extrauterine sarcoma specimens did not assemble together, but rather were scattered within the sarcoma clades (denoted by * on the cladogram in Fig. 1). When the leiomyomas were removed from the comparison, there were 156 synapomorphies delimiting the sarcomas (Table 5).

TABLE 3.

A CLADE OF ALL LEIOMYOSARCOMA SPECIMENS DEFINED BY 20 SYNAPOMORPHIES IN COMPARISON TO NORMAL AND LEIOMYOMA SPECIMENS

A. Overexpressed synapomorphic genes:
X54942	CKS2 CDC28 proteininase regulatory subunit 2	NS
U68566	HAX1 HCLS1 associated protein X-1	NS
L03411	RDBP RD RNA binding protein	OE
X59543	RRM1 ribonucleotide reductase M1 polypeptide	NS
B. Underexpressed synapomorphic genes:
D13639	CCND2, cyclin D2	UE
D21337	COL4A6 collagen, type IV, alpha 6	UE
HG2810-HT2921_at	Csh2 chorionic somatomammotropin hormone 2 [Rattus norvegicus]	NS
L36033	CXCL12 chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)	NS
HG2663-HT2759_at	EMX2 empty spiracles homolog 2 (Drosophila). Homeotic Protein Emx2	NS
HG2663-HT2759_at	Homeotic Protein Emx2	NS
HG2810-HT2921_at	HOXA10 homeobox A10 Expressed in the adult human endometrium	UE
AB002382	LOC284394 hypothetical gene supported by NM_001331	NS
U69263	MATN2 matrilin 2	UE
U85707	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)	UE
Z29678	MITF microphthalmia-associated transcription factor	UE
L35240	PDLIM7 PDZ and LIM domain 7 (enigma)	NS
D87735	RL14 ribosomal protein L14	NS
L14076	SFRS4 splicing factor, arginine/serine-rich 4	UE
J05243	SPTAN1 spectrin, alpha, nonerythrocytic 1 (alpha-fodrin)	NS
C. Dichotomously-expressed synapomorphic genes:
M33197	GAPDH glyceraldehyde-3-phosphate dehydrogenase	NS

Last column reports the status of the synapomorphies as described by Quade et al. (2004) in their significant genes list.

TABLE 4.

A CLADE OF ALL LEIOMYOSARCOMA SPECIMENS DEFINED BY 29 SYNAPOMORPHIES IN COMPARISON TO LEIOMYOMA SPECIMENS ONLY (GDS533)

A. Overexpressed synapomorphic genes:
X54941	CKS1B CD28 protein kinase regulatory subunit 1B	OE
X54942	CKS2 CD28 protein kinase regulatory subunit 2	NS
J03060	GBAP glucosidase, beta; acid, pseudogene	NS
U78027	GLA galactosidase, alpha (associated w/Fabry’s) RPL36A ribosomal protein L36a	NS
Y00433	GPX1 glutathione peroxidase 1	NS
U68566	HAX1 HCLS1 associated protein X-1	NS
X59543	RRM1 ribonucleotide reductase M1 polypeptide	NS
U12465	RPL35 ribosomal protein L35	OE
U67674	SLC10A2 solute carrier family 10 (sodium/bile acid cotransporter family), member 2	NS
B. Underexpressed synapomorphic genes:
U87223	CNTNAP1 contactin associated protein 1	UE
D30655	EIF4A2 eukaryotic translation initiation factor 4A, isoform 2	UE
L20814	GRIA2 glutamate receptor, ionotropic, AMPA 2	UE
M10051	INSR insulin receptor	NS
D79999	LOC221181 hypothetical gene supported by NM_006437	NS
D14812	MORF4L2 mortality factor 4 like 2	UE
L36151	PIK4CA phosphatidylinositol 4-kinase, catalytic, alpha	NS
D42108	PLCL1 phospholipase C-like 1	NS
L13434	RpL41 Ribosomal protein L41	NS
HG921-HT3995_at	Serine/Threonine Kinase, Receptor 2-2, Alt. Splice 3	NS
D31891	SETDB1 SET domain, bifurcated 1	UE
AB002318	Talin2	NS
U53209	TRA2A transformer-2 alpha	NS
D87292	TST thiosulfate sulfurtransferase (rhodanese)	NS
M15990	YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1	NS
C. Dichotomously expressed synapomorphic genes:
U56417	AGPAT1 1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)	NS
M63167	AKT1 v-akt murine thymoma viral oncogene homolog 1	NS
L27560	IGFBP5 insulin-like growth factor binding protein 5	NS
U40223	P2RY4 pyrimidinergic receptor P2Y, G-protein coupled, 4	NS
D76444	RNF103 ring finger protein 103	NS

Last column reports the status of the synapomorphies as described by Quade et al. (2004) in their significant genes list

TABLE 5.

A CLADE COMPOSED OF ALL LEIOMYOSARCOMA SPECIMENS IS DEFINED IN RELATION TO NORMAL SPECIMENS (GDS533)

A. Overexpressed synapomorphic genes:
S78187	CDC25B cell division cycle 25B	NS
U40343	CDKN2D cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	NS
X54942	CKS2 CDC28 protein kinase regulatory subunit 2	NS
X79353	CDI1 GDP dissociation inhibitor 1	NS
X14850	H2AFX H2A histone family, member X	NS
U51127	IRF5 interferon regulatory factor 5	NS
U04209	MFAP1 microfibrillar-associated protein 1	NS
U43177	MpV17 mitochondrial inner membrane protein	NS
U19796	MRPL28 mitochondrial ribosomal protein L28	OE
U37690	POLR2L polymerase (RNA) II (DNA directed) polypeptide L, 7.6 kDa	NS
M22960	PPGB protective protein for beta-galactosidase (galactosialidosis)	NS
U09210	SLC18A3 solute carrier family 18 (vesicular acetylcholine), member 3	NS
M86752	STIP1 stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein)	OE
M26880	UBC ubiquitin C	OE
U43177	UCN urocortin	NS
B. Underexpressed synapomorphic genes:
M12963	ADH1A alcohol dehydrogenase 1A (class I), alpha polypeptide	UE
HG3638-HT3849_s_at	Amyloid Beta (A4) Precursor Protein, Alt. Splice 2, A4(751)	NS
L28997	ARL1 ADP-ribosylation factor-like 1	NS
Z49269	CCL14 chemokine (C—C motif) ligand 14	UE
M92934	CTGF connective tissue growth factor	UE
M74099	CUTL1 cut-like 1, CCAAT displacement protein (Drosophila)	NS
M96859	DPP6 dipeptidyl-peptidase 6	UE
U94855	EIF3S5 eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa	NS
L25878	EPHX1 epoxide hydrolase 1, microsomal (xenobiotic)	NS
U60061-U69140	FEZ2 fasciculation and elongation protein zeta 2 (zygin II)	NS
X67491	GLUDP5 glutamate dehydrogenase pseudogene 5	NS
HG4334-HT4604_s_at	Glycogenin	NS
X53296	IL1RN interleukin 1 receptor antagonist	NS
X55740	NT53 5′-nucleotidase, ecto (CD73)	UE
X78136	PCBP2 poly(rC) binding protein 2	UE
Z50194	PHLDA1 pleckstrin homology-like domain, family A, member 1	NS
J02902	PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform	NS
J03805	PPP2CB protein phosphatase 2, catalytic subunit, beta isoform	NS
U25988	PSG11 pregnancy specific beta-1-glycoprotein 11	NS
M98539	PTGDS prostaglandin D2 synthase 21kDa (brain)	UE
X54131	PTPRB protein tyrosine phosphatase, receptor type, B	NS
M12174	RHOB ras homolog gene family, member B	NS
HG1879-HT3521_at	RHOQ ras homolog gene family, member Q	NS
X98534	VASP vasodilator-stimulated phosphoprotein	NS
X51630	WT1 Wilms tumor 1	UE
HG3426-HT3610_s_at	Zinc Finger Protein Hzf-16, Kruppel-Like, Alt. Splice 1	NS
M92843	ZFP36 zinc finger protein 36, C3H type, homolog (mouse)	UE
C. Dichotomously expressed synapomorphic genes:
U80226	ABAT 4-aminobutyrate aminotransferase	NS
M14758	ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1	NS
M95178	ACTN1 actinin, alpha 1	NS
U76421	ADARB12 adenosine deaminase, RNA-specific, B1 (RED1 homolog rat)	NS
U46689	ALDH3A2 aldehyde dehydrogenase 3 family, member A2	NS
L34820	ALDH5A1 aldehyde dehydrogenase 5 family, member A1 (succinate-semialdehyde dehydrogenase)	NS
M84332	ARF1 ADP-ribosylation factor 1	NS
D14710	ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	NS
X84213	BAK1 BCL2-antagonist/killer 1	NS
U23070	BAMBI BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)	NS
M33518	BAT2 HLA-B associated transcript 2	NS
X61123	BTG1 B-cell translocation gene 1, anti-proliferative	NS
S60415	CACNB2 calcium channel, voltage-dependent, beta 2 subunit	NS
M19878	CALB1 calbindin 1, 28 kDa	NS
L76380	CALCRL calcitonin receptor-like	NS
M21121	CCL5 chemokine (C—C motif) ligand 5	NS
D14664	CD302 CD302 molecule	NS
X72964	CETN2 centrin, EF-hand protein, 2	NS
U66468	CGREF1 cell growth regulator with EF-hand domain 1	NS
M63379	CLU clusterin	NS
X52022	COL6A3 collagen, type VI, alpha 3	UE
L25286	COL15A1 collagen, type XV, alpha 1	NS
S45630	CRYAB crystallin, alpha B	NS
X95325	CSDA cold shock domain protein A	NS
U03100	CTNNA1 catenin (cadherin-associated protein), alpha 1, 102kDa	NS
X52142	CTPS CTP synthase	NS
D38549	CYFIP1 cytoplasmic FMR1 interacting protein 1	NS
X64229	DEK DEK oncogene (DNA binding)	NS
M63391	DES desmin	UE
Z34918	EIF4G3 eukaryotic translation initiation factor 4 gamma, 3	NS
U97018	EML1 echinoderm microtubule associated protein like 1	NS
U12255	FCGRT Fc fragment of IgG, receptor, transporter, alpha	NS
U36922	FOXO1A forkhead box O1A (rhabdomyosarcoma)	NS
U91903	FRZB frizzled-related protein	NS
M33197	GAPDH glyceraldehyde-3-phosphate dehydrogenase	NS
U09587	GARS glycyl-tRNA synthetase	NS
U66075	GATA6 GATA binding protein 6	NS
D13988	GDI2 GDP dissociation inhibitor 2	NS
U31176	GFER growth factor, augmenter of liver regeneration (ERV1 homolog, S. cerevisiae)	NS
U28811	GLG1 golgi apparatus protein 1	NS
U66578	GPR23 G protein-coupled receptor 23	NS
L40027	GSK3A glycogen synthase kinase 3 alpha	NS
U77948	GTF2I general transcription factor II, i	UE
Z29481	HAAO 3-hydroxyanthranilate 3,4-dioxygenase	NS
D16480	HADHA hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit	NS
U50079	HDAC1 histone deacetylase 1	NS
U50078	HERC1 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1	NS
M95623	HMBS hydroxymethylbilane synthase	NS
X79536	HNRPA1 heterogeneous nuclear ribonucleoprotein A1	NS
L15189	HSPA9B heat shock 70 kDa protein 9B (mortalin-2)	NS
U05875	IFNGR2 interferon gamma receptor 2 (interferon gamma transducer 1)	NS
X57025	IGF1 insulin-like growth factor 1 (somatomedin C)	UE
HG3543-	IGF2 insulin-like growth factor 2 (somatomedin A)	NS
U40282	ILK integrin-linked kinase	NS
X74295	ITGA7 integrin, alpha 7	NS
X57206	ITPKB inositol 1,4,5-trisphosphate 3-kinase B	NS
AB002365	KIAA0367	UE
J00124	KRT14 keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)	NS
X05153	LALBA lactalbumin, alpha-	NS
X02152	LDHA lactate dehydrogenase A	NS
HG3527-HT3721_f_at	LHB luteinizing hormone beta polypeptide	NS
X86018	LRRC41 leucine rich repeat containing 41	NS
L38486	MFAP4 microfibrillar-associated protein 4	NS
D87742	MIA3 melanoma inhibitory activity family, member 3	NS
M69066	MSN moesin	NS
AB003177	mRNA for proteasome subunit p27	NS
U47742	MYST3 MYST histone acetyltransferase (monocytic leukemia) 3	NS
M30269	NID1 nidogen 1	NS
U80669	NKX3-1 NK3 transcription factor related, locus 1 (Drosophila)	NS
M10901	NR3C1 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	NS
M16801	NR3C2 nuclear receptor subfamily 3, group C, member 2	NS
U52969	PCP4 Purkinje cell protein 4	UE
J03278	PDGFRB platelet-derived growth factor receptor, beta polypeptide	NS
D37965	PDGFRL platelet-derived growth factor receptor-like	NS
Z49835	PDIA3 protein disulfide isomerase family A, member 3	NS
U78524	PIAS1 protein inhibitor of activated STAT, 1	NS
U60644	PLD3 phospholipase D family, member 3	NS
D11428	PMP22 peripheral myelin protein 22	NS
U79294	PPAP2B phosphatidic acid phosphatase type 2B	NS
S71018	PPIC peptidylprolyl isomerase C (cyclophilin C)	NS
X07767	PRKACA protein kinase, cAMP-dependent, catalytic, alpha	NS
X83416	PRNP prion protein (p27–30)	NS
M555671	PROZ protein Z, vitamin K-dependent plasma glycoprotein	NS
U72066	RBBP8 retinoblstoma binding protein 8	NS
L25081	RHOC ras homolog gene family, member C	NS
U40369	SAT1 spermidine/spermine N1-acetyltransferase 1	NS
M97287	SATB1 special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNAs)	NS
U83463	SDCBP syndecan binding protein (syntenin)	NS
U28369	SEMA3B sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B	NS
HG3925-ht4195_at	SFTPA2 surfactant, pulmonary-associated protein A2	NS
L31801	SLC16A1 solute carrier family 16, member 1 (monocarboxylic acid transporter 1)	NS
M91463	SLC2A4 solute carrier family 2 (facilitated glucose transporter), member 4	NS
U66617	SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1	NS
U50383	SMYD5 SMYD family member 5	NS
D43636	SNRK SNF related kinase	NS
D87465	SPOCK2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2	NS
M61199	SSFA2 sperm specific antigen 2	NS
U15131	ST5 suppression of tumorigenicity 5	NS
U95006	STRA13 stimulated by retinoic acid 13 homolog (mouse)	NS
M74719	TCF4 transcription factor 4	NS
X14253	TDGF1 teratocarcinoma-derived growth factor 1	NS
U52830	TERT telomerase reverse transcriptase	NS
U12471	THBS1 thrombospondin 1	NS
U16296	TIAM1 T-cell lymphoma invasion and metastasis 1	NS
L01042	TMF1 TATA element modulatory factor 1	NS
U03397	TNFRSF9 tumor necrosis factor receptor subfamily, member 9	NS
X05276	TMP4 tropomyosin 4	UE
HG4683-HT5108_s_at	TRAF2 TNF receptor-associated factor 2	NS
U64444	UFD1L ubiquitin fusion degradation 1 like (yeast)	NS
U39318	UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)	NS
X59739	ZFX zinc-finger protein, X-linked	NS

Last column reports the status of the synapomorphies as described by Quade et al. (2004) in their significant genes list

The various combinations of comparisons (several outgroup and ingroup compositions) illustrate the effect of outgroup and ingroup selections on the results (Table 1–Table 5). These comparisons also show the similarities and differences between two diseases that arise within the same tissue, as well as the relationship between the leiomyoma and leiomyosarcoma; and the possibility of the latter arising within leiomyoma.

For the gastric dataset, GDS1210, parsimony analysis produced one most parsimonious cladogram (Fig. 2). The cladogram topology showed two terminal clades with six and five specimens, respectively, and a tandem arrangement of six small clades with the largest having three specimens. The inclusive gastric cancer clade was circumscribed by 34 synapomorphies (Table 6). In a list by list comparison, our 34 identified synapomorphies for the gastric cancer overlapped only with one common gene (CST4) from the gene list of the authors of the study (Hippo et al., 2002).

FIG. 2.

A cladogram of a parsimony phylogenetic analysis of gastric cancer and noncancerous specimens. It shows a clade delineated by 34 synapomorphies (Table 6) encompassing all cancer specimens.

TABLE 6.

A LIST OF 34 SYNAPOMORPHIES DEFINING A CLADE COMPOSED OF ALL GASTRIC CANCER SPECIMENS (GDS1210)

A. Overexpressed synapomorphic genes:
X81817	BAP31 mRNA	No
D50914	BOP1 block of proliferation 1	No
X54667	CST4: cystatin S MGC71923	Yes
L17131	HMGA1 high mobility group AT-hook 1	No
D63874	HMGB1 high-mobility group box 1	No
D26600	PSMB4 proteasome (prosome, macropain) subunit, beta type, 4	No
U36759	PTCRA pre-T-cell antigen receptor alpha PT-ALPHA, PTA	No
X89750	TGIF TGFB-induced factor (TALE family homeobox)	No
B. Underexpressed synapomorphic genes:
X76342	ADH7 alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide ADH-4	No
M63962	ATP4A ATPase, H+/K+ exchanging, alpha polypeptide ATP6A	No
M75110	ATP4B ATPase, H+/K+ exchanging, beta polypeptide ATP6B	No
J05401	CKMT2 creatine kinase, mitochondrial 2 (sarcomeric)	No
L38025	DNTFR ciliary neurotrophic factor receptor	No
M61855	CYP2C9: cytochrome P450, family 2, subfamily C, polypeptide 9 CPC9	No
D63479	DGKD: diacylglycerol kinase, delta 130kDa DGKdelta, KIAA0145, dgkd-2	No
X99101	ESR2 estrogen receptor 2 (ER beta)	No
U21931	FBP1 fructose-1, 6-bisphosphatase 1	No
HG3432-HT3618_at	Fibroblast Growth Factor Receptor K-Sam, Alt. Splice 1	No
M31328	GNB3 guanine nucleotide binding protein (G protein), beta polypeptide 3	No
D42047	GPD1L glycerol-3-phosphate dehydrogenase 1-like	No
M62628	Human alpha-1 Ig germline C-region membrane-coding region, 3′end	No
D29675	Human inducible nitric oxide synthase gene, promoter and exon 1	No
M63154	Human intrinsic factor mRNA	No
Z29074	KRT9 keratin 9 (epidermolytic palmoplantar keratoderma) EPPK, K9	No
X05997	LIPF lipase, gastric	No
U50136	LTC4S leukotriene C4 synthase MGC33147	No
X76223	MAL: mal, T-cell differentiation protein	No
U19948	PDIA2 protein disulfide isomerase family A, member 2	No
L07592	PPARD peroxisome proliferative activated receptor, delta	No
U57094	RAB27A, member RAS oncogene family	No
AC002077	SLC38A3 solute carrier family 38, member 3	No
Z29574	TNFRSF17 tumor necrosis factor recepter superfamily, member 17	No
C. Dichotomously expressed synapomorphic genes:
D00408	CYP3A7 cytochrome P450, family 3, subfamily A, polypeptide 7 CP37, P450-HFLA	No
U29092	SELENBP1 selenium binding protein 1	No

Synapomorphies include: 8 OE genes, 24 UE genes, and 2 DE genes in comparison with the normal specimens. Last column reports the status of the synapomorphies as described by Hippo et al. (2002). Yes = listed; No = not listed.

Interplatform concordance

Testing of interplatform concordance was carried out by comparing the two lists of synapomorphies obtained from two leiomyoma studies, GDS484 and GDS533 (comparison results are summarized in Table 7 and Table 8). Out of the ~22,000 genes in the GDS484 dataset, our analysis produced a total of 1485 synapomorphic genes circumscribing the leiomyoma specimens. Although the leiomyomas of the GDS533 were delimited by 146 synapomorphies out of ~7,000 gene probes, a comparison between the two sets of leiomyomas’ synapomorphies produced 45 shared ones between the two (Table 7 and Table 8 ), a 31% concordance in synapomorphies despite the sizable difference in the number of probes between the two datasets, which is still better than the 12% concordance between the statistically produced gene lists of the two published studies (Hoffman et al., 2004; Quade et al., 2004).

TABLE 8.

SUMMARY OF CONCORDANCE RESULTS BETWEEN GDS484 AND GDS533

		GDS533 (Fibroids and Leiomyosarcomas)
		Quad et al. Gene List	Abu-Asab et al. Synapomorphies for Fibroids (146)	Abu-Asab et al. Synapomorphies for Fibroids and Leiomyosarcoma (32)
GDS484 (Fibroids)	Hoffman et al. Gene List	12%	18%	19.3%
	Abu-Asab et al. Synapomorphies for Fibroids (1485)	20%	31%	48%
GDS533 Quad et al. Gene List		N/A	16.5%	45%

The comparisons were carried out in various combinations: statistical versus statistical, phylogenetic versus statistical, and phylogenetic versus phylogenetic. N/A: not applicable (number of synapomorphies).

Furthermore, 48% concordance resulted when comparing the 32 synapomorphies of the leiomyomas and leiomyosarcomas clade (GDS533; Table 1) with the 1485 synapomorphies of the leiomyomas of GDS484 (Table 7); the clades’ synapomorphies overlapped as follows: 1/1 OE, 7/8 UE (except FOSB), and 8/23 DE, an 89% concordance within the OE and UE and 35% within the DE. Additionally, there was 45% concordance between the 32 synapomorphies of the leiomyomas and leiomyosarcomas clade and the gene list of Quad et al. (2004) (Table 8).

However, a lower concordance was obtained when comparing the phylogenetic synapomorphies against statistically generated gene lists. The synapomorphies of leiomyomas (GDS533; Table 2) showed 18% concordance (4/25 OE, 8/42 UE) with the 78 significant genes of Hoffman et al. (2004; GDS484, gene list produced by fold change), and 16.5% (5/25 OE, 6/42 UE) with the 146 genes of Quad et al. (2004; GDS533, gene list produced by an F statistic). This was higher than the concordance between the two gene lists of the published uterine studies, 12% (3/25 OE, 5/42 UE). The two studies had no mention of DE genes.

Data pooling and interplatform comparability

Data pooling and interplatform comparability was carried out on the combined polarized matrices of the gastric (GDS1210) and uterine (GDS533) datasets. Their inclusive parsimony analysis produced one most parsimonious cladogram (Fig. 3). Its topology showed a total separation of the gastric cancer from the uterine leiomyoma and sarcoma specimens into two large clades. However, the two types of cancers shared 16 synapomorphies that delimited a clade composed of all the gastric and uterine specimens (Table 9).

FIG. 3.

A cladogram representing a comparability analysis of the gastric (GDS1210) and uterine (GDS533) datasets. The polarized matrices of the two datasets were pooled together and processed by the parsimony phylogenetic algorithm, MIX. Each of the cancers (gastric and leiomyosarcoma) forms its own clade, and the inclusive clade encompassing the two cancers and leiomyomas is delimited by a set of synapomorphies (Table 9).

TABLE 9.

INTERPLATFORM COMPARABILITY

ID	Gene
U52522	ARFIP2 ADP-ribosylation factor interacting protein 2 (arfaptin 2)
U51478	ATP1B3 ATPase, NaK transporting, beta 3 polypeptide
X66839	CA9 carbonic anhydrase IX
M60974	GADD45A growth arrest and DNA-damage-inducible, alpha
X01677-M33197	GAPDH glyceraldehyde-3-phosphate dehydrogenase [two readings]
X14850	H2AFX H2A histone family, member X
U52830	Homo sapiens Cri-du-chat region mRNA, clone CSC8
U25138	KCNMB1 potassium large conductance calcium-activated channel, subfamily M, beta member 1
D21063	MCM2 minichromosome maintenance deficient 2
L38486	MFAP4 microfibrillar-associated protein 4
D87463	PHYHIP phytanoyl-CoA 2-hydroxylase interacting protein
X02419	PLAU plasminogen activator, urokinase
L48513	PON2 paraoxonase 2
U29091	SELENBP1 selenium binding protein 1
Z19083	TPBG trophoblast glycoprotein
M25077	TROVE2 TROVE domain family, member 2

A list of 16 synapomorphies defining a clade composed of all gastric cancer (GDS1210) as well as uterine sarcoma and leiomyom specimens (GDS533).

The resulting inclusive cladogram (Fig. 3) showed an almost total agreement with the single type cladograms (Fig. 1 and Fig 2), indicating a successful pooling of datasets. However, there was a slight variation in the topology of minor branches between the cladogram of Figure 2 and the inclusive one of Figure 3. These slight differences are most likely due to the increased number of normal specimens that were used in outgroup of the inclusive cladogram. Outgroup size used here was by no means ideal; the larger the membership of the outgroup the more stable the topology of the generated cladogram (Graybeal, 1998).

Discussion

Microarray data analysis aims to identify differentially expressed genes, and subsequently characterize genetic patterns, classify specimens accordingly, and point out potential biomarkers. However, most of the problems that are currently associated with microarray analysis arise from using only the quantitative aspect of the data (the absolute continuous data values of gene expression) to carry out parametric statistical analysis. Such a statistical analysis forecasts gene linkage on the basis of quantitative correlation and not expression pattern, and lacks the power to recognize and utilize specific gene expression patterns such as dichotomous-expression and partial asynchronicities (Abu-Asab et al., 2008; Allison et al., 2006). This results in discrepancies that affect which genes are considered differentially expressed by the two main ranking criteria for generating gene lists, the t-test and fold change (Guo 2006). Our phylogenetic analysis supports a qualitative approach where the directionality of expression is the first step to designate the expression value as significant, followed by parsimony search to plot a classification of specimens with the smallest number of steps that explains the data’s distribution pattern.

This parsimonious analysis produced higher interplatform concordance than the gene lists generated with t-test and fold change (Table 7 and Table 8), and allowed the pooling and comparability of two independent experiments. Such results confer reliability to a qualitative parsimonious approach to analyzing gene expression data. Table 10 summarizes the major characteristics of a parsimony phylogenetic approach.

TABLE 10.

SUMMARY OF THE CHARACTERISTICS OF A PARSIMONIOUS PHYLOGENETIC ANALYSIS THROUGH POLARITY ASSESSMENT OF GENE-EXPRESSION VALUES FOLLOWED BY A MAXIMUM PARSIMONY ANALYSIS

•	Offers a qualitative assessment of microarray gene expression data by sorting expression values into derived or ancestral.
•	Identifies synapomorphies (shared derived expression states) and uses them to delineate clades (class discovery). Synapomorphies are also the potential biomarkers.
•	Searches for the most parsimonious classification of specimens; the one with minimum number of steps, reversals, and parallels.
•	Efficiently models the heterogeneous expression profiles of the diseased specimens. Those with fast mutation rate such as cancer.
•	Incorporates gene expressions that violate normal distribution in a set of specimens—e.g., dichotomously expressed genes.
•	Reduces the sensitivity to experimental noise.
•	Permits pooling of multiple experiments.
•	Allows intra and intercomparability of data.
•	Produces higher concordance between gene lists than statistical methods (F & t-statistics and fold change).
•	Offers a nonparametric data-based, not specimen-based, gene listing and gene linkage.

In addition to its evident scientific applications, a phylogenetic analysis as outlined here has clinical implications as well. Indeed, the results of the three microarray gene expression datasets show the clinical potential for such parsimonious analysis; they produced a total distinction of the sarcoma from the fibroid tissues (the leiomyomas), and these two classes from gastric cancer. It also identified a number of synapomorphies for gastric and uterine cancers, thus defining each as a separate disease entity with its unique shared derived expressions (see also Meza-Zepeda et al. 2006, for further support of this point). Furthermore, the combined analysis revealed the shared alterations of gene expression that are shared between the uterine and gastric cancers (Table 9). This conclusion is supported by the presence of these synapomorphic gene expressions as significant ones in other types of cancers as well: bladder, breast, colorectal, ovarian, pancreatic, prostate, and renal (Guzińska-Ustymowicz et al., 2008; Dong et al., 2007; Huang et al., 2006; Pilarsky et al., 2004).

Advantages of polarity assessment

There are several reasons for our preference of a combination of polarity assessment via outgroup comparison and parsimony over other methods for the analysis of gene expression microarray data, an approach that is also supported by other authors (Allison et al., 2006; Kolaczkowski and Thornton, 2004). Parsimony phylogenetic analysis requires polarity assessment for each data value to determine its novelty—whether it represents a change from the normal state (Abu-Asab et al., 2008). We advocate that qualitative, and not only quantitative, similarity is a better measure of common ontogenetic steps among specimens, and that a correlation of genes based on similar quantitative expression is not necessarily indicative of ontogenic relationships among genes.

Polarity assessment does not set an arbitrary stringency on gene selection, especially where the distribution pattern is gene specific within a set of specimens (e.g., DE and partially asynchronous genes), while other methods are not optimal for its assessment (Huang and Qu, 2006; Lyons-Weiler et al., 2004). Fold change and F and t-statistics may dismiss from the gene list those genes with dichotomous expressions, although they are indicative of a unique expression type and may account for some phenomena such as transitional clades located between diseased and normal clades, and multiple developmental pathways in some disease types (Abu et al., 2006; Lyons-Weiler et al., 2004). The gene lists of Table 1C–Table 7C show a large number of DE asynchronous genes that were mostly not considered significant by other methods (Hippo et al., 2002; Hoffman et al., 2004; Quade et al., 2004), or their dichotomous mode was not noticed by the authors.

Because polarity assessment transforms the quantitative data into a qualitative matrix, it reduces the data noise. The absolute quantitative nature of the microarray data restricts their use and interpretation due to their range of inconsistencies between runs, platforms, and laboratories. By polarizing each data set with its own set of outgroup specimens, the inconsistencies of the experiment are eliminated since the polarization process is a comparison between equals—data values generated at the same time. The benefit here translates into the ability to pool a large number of experiments, carry out intra- and interplatform comparabilities, and a better gene list concordance between experiments. However, as discussed below, polarity assessment is sensitive to the choice and size of the outgroup specimens.

Selection and size of the outgroup

When conducting a polarity assessment, outgroup’s selection and its effective size are very significant factors in correctly identifying synapomorphies, and therefore, optimally delimiting the classes of diseased specimens. The composition of the outgroup specimens affects the outcome of the analysis as demonstrated by the different combinations of outgroups that we used to conduct polarity assessment for the leiomyosarcomas and leiomyomas (Table 1–Table 5). We selected these various arrangements of outgroups to demonstrate that their compositions produced slightly different but still biologically meaningful results. It is important to note that the outgroup should be composed of only healthy specimens when the goal is to find out the genes involved in disease inception, progression, and maintenance. As Table 1–Table 5 show, variations of out/ingroup composition lead to variations in identifying synapomorphies. Also, Figure 3 shows that the different types of cancers will separate into their respective clades when the outgroup is composed of normal specimens; a process that can be utilized for diagnosis.

In our combined analysis (Fig. 3), the increase in outgroup size did not affect the major topology of the cladogram, but rather the internal branching of some clades (normal and gastric cancer) when compared with their single analysis (Fig. 1–Fig 2). Because increasing the number of genes in the study does not have the same effect as enlarging outgroup size (Graybeal, 1998), it is our conclusion that a successful analysis requires a good number of normal specimens to be used as the outgroup. For microarray experiments to be meaningful and provide high predictivity, the smallest number of normal specimens that encompasses the maximum variation per population should be established and used in the analysis.

Inferring gene linkage through parsimony phylogenetic analysis

Whereas gene linkage of a clustering dendrogram is based on quantitative correlations between differentially expressed genes, in a parsimony cladogram it is based on the distribution of derived and ancestral gene expression states of all genes of all the specimens; that is, it is a map of expression states—both ancestral and derived. It reflects the classification that has the lowest number of steps as well as parallels and reversals to explain the distribution of expression states among specimens.

Gene linkage here is based on the location of genes on the cladogram. The synapomorphies below a node on the cladogram are the linked genes that are shared among the specimens above that node. Because a parsimonious cladogram is hierarchical, every one of its nodes has its synapomorphy( ies). This characteristic of a cladogram presents it as a map of linked genetic alterations that produce the diversity/relatedness of its specimens and may also permit the tracing of shared ontogenic pathways that are responsible for disease initiation and progression.

Improved interplatform concordance and comparability

Improved interplatform concordance is a criterion that will confer robustness and significance on microarray as a valid experimental and clinical platform. Our tests of concordance by comparing the lists of synapomorphies generated by polarity assessment of two experiments produced better results than those of fold change and F-statistic, and better than between the latter two (Table 8). When comparing the synapomorphies of a clade composed of leiomyomas and leiomyosarcomas (GDS533) with the synapomorphies of leiomyomas (GDS484), we obtained a high concordance of 89% within over- and underexpressed and 35% within dichotomously expressed genes. The concordance between the two studies could have been higher if the number of probes of the GDS533 was closer to GDS484–7,000 versus 22,000 (Hoffman et al., 2004; Quade et al., 2004). Furthermore, even a comparison of the synapomorphies of two leiomyoma groups [GDS484 (1485 synapomorphies) and GDS533 (146 synapomorphies; Table 2)] produced 31% concordance between the two groups of leiomyoma (45/146; Table 7). Nevertheless, this was a higher percentage than was produced by statistical methods (12%).

Interplatform comparability has been difficult to carry out on microarray data because of data inconsistencies between runs, experiments, and laboratories; however, with polarity assessment, which converts the quantitative values of gene expression of every experiment into a qualitative matrix, it is possible to combine several matrices and carry out intra-and interplatform comparisons in a parsimonious phylogenetic sense. A phylogenetic interplatform comparability of microarray data can be carried out if each dataset can be polarized separately with its own outgroup to produce its polarized matrix. Furthermore, when their probes are identical, two or more polarized sets can be pooled together and analyzed as Figure 3 shows. We have successfully pooled and analyzed two separately polarized datasets (GDS533 and 1210) of gastric cancer as well as uterine leiomyoma and leiomyosarcoma, where the two datasets were prepared separately but on an identical gene chip platform, GPL80.

Implications on disease definition, profiling, diagnosis, and prognosis

Although it is assumed that each disease has its own unique developmental pathway(s) (Adsay et al., 2002; Chung, 2000; Hayashi et al., 2004), thus far, the omics data has not been used to prove this premise. Our analysis of two independently generated datasets that represent uterine (GDS533) and gastric (GDS1210) cancers confirms that each of these two types of cancer is a natural class of specimens (a clade) that is circumscribed by its own set of synapomorphies. If this can be extended to other types of cancer, then each cancer can be considered a natural clade with its unique gene expression identifiers—the synapomorphies.

There are several implications to this conclusion; the most obvious is its effect on the definition of biomarkers. If the specimens of a type of cancer form a clade, then any suggested biomarker has to be selected from the clades’ synapomorphies; otherwise, it will not be a universal diagnostic test for all the specimens of this cancer. Some of the currently applied immunohistomarkers are not universal synapomorphies. For example, the memberships of all four clades of the gastric cancers (Fig. 2) did not correlate well with the specimens’ immunoreactivity to antibodies against p53, E-cadherin, and β-catenin, and a published two-way clustering did not correlate any better (Hippo et al., 2002). The discordance between omics biomarkers and most of the currently used immunohistological markers is a problem that can be better addressed in a phylogenetic sense. The discordance between microarray and immunohistochemical (IHC) biomarkers is due to the differing natures of these two types of markers. Although gene-expression biomarkers are based on the averaging of the expression values of the number of the cells used in the study (i.e., the cell homogenate), the IHC is based on the pathologist reading of the percentage of positive cells in the stained section. The IHC result is given as a percentage figure that could start at 10%, and is used to associate the neoplasm with the normal tissue of origin. For an accurate and meaningful interpretation of the gene expression analyses, a comparison between the two types of biomarkers should be avoided, and the phylogenetic concept that is suggested here should be adopted.

A second implication is that a phylogenetic classification can be a clinical tool to carry out early detection, diagnosis, grading, prognosis, and posttreatment evaluation; these tasks can be realized through a parsimony analysis where the place of a specimen within the cladogram (i.e., the classification) will indicate its pathologic status. Alternatively, the health status of a specimen can be probed by using the synapomorphies as the biomarkers of the disease, that is, through class prediction by assigning the specimen to a clade. Because the cladogram also indicates the direction of change in gene expression among the specimens, it places those specimens with the advanced number of derived gene expression patterns at the terminal end of the cladogram, and places the specimens with the least number of gene expression changes at the lower end of the cladogram, and it may be developed for use in grading, prognosis, targeted treatment, and posttreatment assessment.

Additionally, the phylogenetic classification is a dynamic and seamless tool that will incorporate a novel specimen by placing it in the proximity of its sister groups, depending on the number of synapomorphies it shares with other members of a clade, without any radical alteration to the topology of the cladogram.

Resolving standing questions through parsimony phylogenetics: an example

Our analysis of uterine fibroids and sarcomas illustrates how a parsimony phylogenetic analysis may confront some of the unresolved issues in bioinformatics and medicine. For example, one of the persistent questions in pathology is the relationship between leiomyoma and leiomyosarcoma (Quade et al., 2004). It has been reported that approximately 1% of leiomyosarcoma may have arisen in preexisting leiomyoma (Lee et al., 2005). By analyzing data of normal uterus, leiomyoma, and leiomyosarcoma, we demonstrated that the latter two share a number of synapomorphies and form together an inclusive clade (Table 1 and Fig. 1 and Fig 3), and that leiomyosarcoma has an additional number of synapomorphies distinguishing them from leiomyoma (Table 3). Although the leiomyoma specimens, when analyzed alone, without the leiomyosarcoma, appear to have a large number of synapomorphies (Table 2), these synapomorphies are not unique to leiomyoma. Leiomyoma as a group does not form a clade within a comprehensive ingroup that includes the leiomyosarcoma; there is not even one gene expression that is unique to the group itself in this context. Because it shares with the leiomyosarcoma its synapomorphies, leiomyoma may be considered an incipient form of leiomyosarcoma.

Conclusion

The application of phylogenetic analysis through polarity assessment and parsimony to several gene expression microarray datasets provides the basis for a new paradigm to analyzing and interpreting microarray data (Table 10). It offers an alternative to F and t-statistics and fold change methods of generating differentially expressed gene listing and statistical gene linkage, brings out a higher interplatform concordance, resolves interplatform comparability problems, defines biomarkers as synapomorphies, circumscribes disease types as clades defined by synapomorphies, and possibly transforms microarray into diagnostic, prognostic, and posttreatment evaluation tool.