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. Author manuscript; available in PMC: 2020 Jul 1.
Published in final edited form as: Cancer Res. 2019 May 21;79(13):3514–3524. doi: 10.1158/0008-5472.CAN-18-2047

Table 2:

Isoform expression-drug activity pairs wth enhanced correlations to isoforms as compared to composite gene expression

Gene
 Transcript
 Protein
 Drug
 Gene expression vs. drug activity P values i
Names a Type b RefSeq c Abundance d Amino Acids e Drug Name f NSC g Mech.(s) of action h Isoform Composite
BCR GTPase-activating NM_021574 0.13 1227 / 1271 Imatinib 743414 BCR-ABL|PK:YK 0.00001 0.2036
CASP1 Apoptotic NM 001257119 0.216 383 / 404 Imexon 714597 Apo 0.00005 0.00201
CASP8 Apoptotic NM_001080124 0.151 464 / 479 Arsenic trioxide 92859 Apo 0.00092 0.74096
MAPK8 Apoptotic NM_001278548 0.277 308 / 427 Oxaliplatin 266046 AlkAg 0.00002 0.04352
API5 Survival NM_006595 0.290 504 / 524 Dasatinib 759877 PK:YK,PDGFR,KIT 0.00010 0.34951
ALKBH2 DDR NM_001001655 0.200 157 / 261 Benzaldehyde (BEN) 281612 AlkAg 0.00104 0.32629
DDX11 DDR NM_004399 0.160 856 / 970 Bendamustine 138783 AlkAg 0.00313 0.41420
POLD3 DDR NR_046409 0.122 na Ifosfamide 109724 AlkAg 0.00002 0.04390
CDK1 Protein kinase NM_033379 0.088 240 / 297 Palbociclib 758247 PK:STK,CDK 0.00010 0.01554
CDK20 Protein kinase NM_001039803 0.229 346 / 346 Palbociclib 758247 PK:STK,CDK 0.00001 0.00206
AKT3 Protein kinase NM_001206729 0.099 465 / 479 Vandetanib 760766 PK:YK,EGFR 0.00056 0.20447
PDPK1 Protein kinase NM_031268 0.360 429 / 556 7-Hydroxystaur. 638646 PK:STK 0.00225 0.39567
MAPK10 Protein kinase NM_002753 0.49 422 / 464 AZD-9291 779217 PK:EGFR 0.00005 0.01349
FGFR3 Signalling NM_022965 0.253 694/806 Pazopanib 752782 PK:YK,PDGFR,FGFR 0.00003 0.00780
a

Gene name as defined by the UCSC Table Browser at https://genome.ucsc.edu/cgi-bin/hgTables.

b

DDR is DNA damage repair. Chromatin is chromatin modifying. MT is methylation transferase. Genes may fall into additional functional categories.

c

Transcript reference sequence as defined by NCBI at http://www.ncbi.nlm.nih.gov/nucleotide.

d

Abundance of isofrom as compared to other isoforms for the same gene.

e

Number of amino acids in protein.

f

All drugs are either Food and Drug Administration approved or in clinical trial. 7-Hydroxystaur. is 7-Hydroxystaurosporine.

g

Cancer Chemotherapy National Service Center (NSC) number.

h

Mech. is mechanism. Apo is apoptosis inducer. AlkAg is alkylating agent. PK is protein kinase inhibitor. YK is tyrosine kinase inhibitor. PDGFR is PDGFR inhibitor. KIT is KIT inhibitor. Db is DNA binder. T2 is topoisomerase 2 inhibitor. STK is Serine threonine kinase inhibitor. CDK is CDK inhibitor. EGFR is EGFR inhibitor. PDGFR is PDGFR inhibitor. BRAF is BRAF inhibitor. HDAC is histone deacetylase. FGFR is FGFR inhibitor.

i

Calculated from Pearson’s correlations. The FPKM values for both composite gene and isoform expression is were log2 transformed to make appropriate comparison to the log10 transformed drug activity data.