. 2012 Sep 20;3:310. doi: 10.3389/fmicb.2012.00310

Table 2.

Significantly affected HeLa cell proteins after reovirus infection.

Accession	HGNC ID	Name	Cytoplasm					Nucleus
				Standard		Proteominer			Standard		Proteominer
			Inf/Mock¹	# Peps	z-Score	#Peps	z-Score	Inf/Mock¹	# Peps	z-Score	# Peps	z-Score
UP-REGULATED PROTEINS
Proteins detected in multiple similar fractions
gi\|8923450	SDHAF2	Succinate dehydrogenase assembly factor 2, mitochondrial precursor	50.6	4	24.036¹	4	0.526
gi\|222136619	MX1	Myxovirus resistance protein 1	6.12	6	6.583	6	8.839	42.0	2	21.873	3	5.234
gi\|116534937	IFIT1	Interferon-induced protein with tetratricopeptide repeats 1 isoform 2	6.45	6	9.877	4	7.414	2.67			2	4.227
gi\|55741675	K0907	Hypothetical protein LOC22889						4.59	3	−0.368	3	9.139
gi\|4826649	RM49	Mitochondrial ribosomal protein L49	4.58	2	10.901	2	0.178	0.95			8	−0.266
gi\|4826774	ISG15	ISG15 ubiquitin-like modifier	3.80	10	7.170	5	5.083	3.29			4	5.131
gi\|27881482	DDX58	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide RIG-I	3.77	2	6.322	2	5.832
gi\|6274552	STAT1	Signal transducer and activator of transcription 1 isoform alpha	2.76	19	5.372	8	3.952	1.81	3	−1.456	6	3.663
gi\|72534658	IFIT3	Interferon-induced protein with tetratricopeptide repeats 3	2.57	2	0.803	5	4.660	1.02			1
gi\|19743875	FUMH	Fumaratehydratase precursor	1.02	25	0.240	16	−0.136	2.24	4	5.851	4	0.098
gi\|4507241	SSRP1	Structure specific recognition protein 1	2.12	8	2.640	1		0.01	2	−21.042
gi\|4506103	E2AK2	Eukaryotic translation initiation factor 2-alpha kinase 2 isoform a	1.95	6	2.760	10	3.010	1.59			6	1.972
gi\|4506003	PP1A	Protein phosphatase 1, catalytic subunit, alpha isoform 1	0.94	23	−0.352			1.91	3	4.587	3	0.699
gi\|112789562	IF16	Interferon, gamma-inducible protein 16	1.70	7	2.314	3	2.858	1.90	7	2.219	4	3.824
gi\|42516576	GLRX5	Glutaredoxin 5	1.84	3	1.658	4	3.180
gi\|166706903	GBP1	Guanylate binding protein 1, interferon-inducible, 67 kDa	1.81	10	2.380	9	2.933
gi\|38016914	SAMH1	SAM domain- and HD domain containing protein 1	1.71	2	4.006	4	1.599
gi\|50592994	THIO	Thioredoxin	0.98	8	−0.430	11	0.070	1.69	2	−0.620	6	2.876
gi\|48762920	K6PL	Liver phosphofructokinase	1.69	5	0.603	3	3.920
gi\|52630342	1C07	Major histocompatibility complex, class I, C precursor	1.67	14	0.382	16	3.194	1.27			3	1.007
gi\|22035653	APOL2	Apolipoprotein L2	1.64	3	2.583	2	1.951
gi\|5031777	IDH3A	Isocitrate dehydrogenase 3 NAD(+) alpha precursor	0.97	18	−0.385	15	0.062	1.57	2	2.162	2	1.892
gi\|223718097	OXA1L	Oxidase (cytochrome c) assembly 1-like	1.57	1		2	2.576
gi\|19923973	KCD12	Potassium channel tetramerization domain containing 12	1.07	7	0.328			1.57	2	1.969	3	1.999
gi\|4758786	NDUS2	NADH dehydrogenase (ubiquinone) Fe-S protein 2	1.55	3	2.985	2	0.692	1.56			3	1.880
gi\|5031863	LG3BP	Galectin 3 binding protein	1.55	7	1.474	13	2.083
gi\|62530384	ECI1	dodecenoyl-Coenzyme A delta isomerase precursor	0.99	12	−0.313	2	0.730	1.55	4	2.281	3	1.564
gi\|9506689	EXOS4	Exosome component 4	1.08			5	0.297	1.53	2	4.810	5	0.132
Proteins detected multiple times/regulated at least once
gi\|33356547	MCM2	Minichromosome maintenance complex component 2	1.13	28	0.439	28	0.584	8.04			3	9.026
gi\|5453740	ML12A	Myosin, light chain 12A, regulatory, non-sarcomeric	6.89	13	10.050			0.84			10	−0.811
gi\|24307901	IFI35	Interferon-induced protein 35	3.71	2	6.811			3.04	3	5.269
gi\|5174513	SMAD3	mothers against decapentaplegic homolog 3 isoform 1	1.23			1		2.03			3	3.044
gi\|4503049	CRIP2	Cysteine-rich protein 2	1.99			4	2.809	1.18			3	0.677
gi\|148747351	PACN2	Protein kinase C and casein kinase substrate in neurons 2	1.70	3	2.742			1.04			2	0.103
gi\|21956645	MTPN	Myotrophin	1.07	3	0.323			1.68			2	2.211
gi\|33469966	SCFD1	Vesicle transport-related protein isoform a	0.98	3	1.814	8	−0.875	1.68	4	2.439
gi\|5902076	SRSF1	Splicing factor, arginine/serine-rich 1 isoform 1	1.63			2	1.994	1.07	14	0.109	25	0.336
gi\|39780588	TSR1	TSR1, 20S rRNA accumulation	1.00	1				1.58	4	2.147
gi\|13540606	CLPB	Caseinolytic peptidase B	1.52	2	2.158			0.49	1
Proteins detected once
gi\|17921993	TBA3C	Tubulin, alpha 3c	100	86	24.036
gi\|31543983	ARFG2	ADP-ribosylation factor GTPase activating protein 2						5.73	3	8.278
gi\|4758442	GMFB	Glia maturation factor, beta	3.03	2	5.754
gi\|19923597	SP130	Sin3A-associated protein, 130 kDa isoform b						2.49	2	4.318
gi\|13375616	FADS3	Fatty acid desaturase 3	2.14	2	3.931
gi\|74271837	GLNA	Glutamine synthetase	2.01			3	2.852
gi\|4502209	ARF5	ADP-ribosylation factor 5						1.90			3	2.747
gi\|70608211	NT5C3	5(-Nucleotidase, cytosolic III isoform 2	1.88			3	2.587
gi\|20631967	BAX	Apoptosis regulator BAX isoform sigma	1.87			2	2.559
gi\|4757876	BST2	Bone marrow stromal cell antigen 2						1.87			4	2.666
gi\|222144328	MYL12B³	Myosin regulatory light chain MRCL2 isoform B						1.83	6	2.847
gi\|53828918	PGTA	Rabgeranylgeranyltransferase alpha	1.83			2	2.459
gi\|190014625	RRP44	DIS3 mitotic control isoform b						1.81	2	2.810
gi\|5729820	SYFM	Phenylalanyl-tRNAsynthetase 2 precursor	1.79			2	2.382
gi\|4505467	NT5E	5′ Nucleotidase isoform 1 preproprotein						1.74	2	2.618
gi\|4505895	PLRG1	Pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)						1.71	2	2.540
gi\|4505587	PA1B3	Platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit	1.67	2	2.634
gi\|28395033	RHOC	Ras homolog gene family, member C precursor	1.62			18	1.981
gi\|148536825	CO4A1	Alpha 1 type IV collagen preproprotein	1.59	2	2.380
gi\|71044479	DIDO1	Death inducer-obliterator 1 isoform c						1.58	3	2.153
gi\|9955963	ABCB6	ATP-binding cassette, sub-family B, member 6	1.56	4	2.294
gi\|56676335	RIF1	RAP1 interacting factor 1						1.56	2	2.083
gi\|40254978	FIP1	FIP1 like 1 isoform 1						1.54	4	2.041
gi\|7706481	CAB39	Calcium binding protein 39	1.54	5	2.203
gi\|221316634	LMO7	LIM domain only 7 isoform 2						1.53	6	1.991
gi\|194473714	LXN	Latexin	1.52	3	2.155
gi\|8923219	TRM1	tRNAmethyltransferase 1 isoform 1	1.50	6	2.072
DOWN-REGULATED PROTEINS
Proteins detected in multiple similar fractions
gi\|4507241	SSRP1	FACT complex subunit SSRP1	2.12	8	2.640	1		0.012	2	−21.042
gi\|4506457	RCN2	Reticulocalbin 2 precursor	0.86	14	−0.076	27	−0.993	0.32			2	−4.994
gi\|4505751	PROF2	Profilin 2 isoform b	0.91	8	−0.215	9	−0.601	0.46			3	−3.447
gi\|7661832	SSU72	Ssu72 RNA polymerase II CTD phosphatase homolog	0.84	3	−1.873	3	−0.127	0.52			3	−2.902
gi\|4506929	SH3G1	SH3 domain GRB2-like 1	0.57	5	−3.424	3	−1.835	27.85	3	21.873	8	−1.062
gi\|72534660	SRSF7	Splicing factor, arginine/serine-rich 7	0.57	2	0.155	5	−3.972	0.91	6	−1.680	12	0.031
gi\|7661672	PDIP2	DNA polymerase delta interacting protein 2	0.88	5	−0.696	3	−0.516	0.58			2	−2.426
gi\|4758340	SYFA	Phenylalanyl-tRNAsynthetase, alpha subunit	0.96	9	−0.532	13	−0.003	0.58	4	−2.095	6	−2.721
gi\|31543415	G45IP	Growth arrest and DNA-damage-inducible, gamma interacting protein 1						0.60	3	−21.042	4	0.149
gi\|45359846	G3BP2	Ras-GTPase activating protein SH3 domain-binding protein 2 isoform b						0.60	12	−3.099	9	−1.520
gi\|4507467	BGH3	Transforming growth factor, beta-induced, 68kDa precursor	0.64	7	−3.152	6	−1.196	0.82			5	−0.890
gi\|40353740	LARP4	La-related protein 4 isoform b	0.65	1		3	−2.585	1.27			2	0.997
gi\|4503523	EIF3D	Eukaryotic translation initiation factor 3 subunit D	1.07	8	0.672	3	−0.582	0.66	4	−2.237	1
Proteins detected multiple times/regulated at least once
gi\|16554629	WDR5	WD repeat domain 5	0.011	4	−23.627			1.00	2	0.001	2	−0.034
gi\|4502337	ZA2G	Alpha-2-glycoprotein 1, zinc	0.11			2	−8.924	0.012			2	−19.301
gi\|60097902	FLG	Filaggrin	0.01			2	−18.099	1.99			1
gi\|4557894	LYSC	Lysozyme precursor	0.11			5	−8.960	0.17			1
gi\|4505821	PIP	Prolactin-induced protein	0.33			3	−4.601	0.29			2	−5.451
gi\|58530840	DESP	Desmoplakin isoform I	0.30			11	−4.902	0.47			2	−3.371
gi\|8922652	ARFG1	ADP-ribosylation factor GTPase activating protein 1 isoform a	1.07			4	0.290	0.46			2	−3.437
gi\|116235460	YTHD3	YTH domain family, member 3	0.50			4	−2.822	0.88	5	−3.099	11	0.145
gi\|13129040	SPATA5L1	Spermatogenesis associated 5-like 1	1.12			2	0.454	0.52	2	−3.090
gi\|145580575	CTBP2	C-Terminal binding protein 2 isoform 2	1.07			9	0.282	0.53			4	−2.827
gi\|4826730	MTOR	FK506 binding protein 12-rapamycin associated protein 1	0.99	2	−0.092			0.55	4	−2.860
gi\|47271443	SRSF2	Splicing factor, arginine/serine-rich 2	0.56	4	−3.068			1.35	5	−1.187	3	3.590
gi\|4506901	SRSF3	Splicing factor, arginine/serine-rich 3	0.60			5	−2.120	0.99	12	0.465	17	−0.448
gi\|4885245	FOSL2	FOS-like antigen 2	0.91			2	−0.402	0.60			2	−2.271
gi\|20127486	PLIN3	Perilipin-3 isoform 1	1.00	24	−0.045			0.61	3	−2.391
gi\|7657176	CNPY2	Canopy 2 homolog	0.96	12	−0.242			0.61	2	−2.337
gi\|56118310	NUCKS	Nuclear casein kinase and cyclin-dependent kinase substrate 1	1.01	4	0.017			0.66	6	−2.022
gi\|89276751	CO5A1	Alpha 1 type V collagen preproprotein	0.86	10	−0.815			0.66	3	−2.022
Proteins detected once
gi\|4885477	MYG	Myoglobin	0.012			2	−18.099
gi\|61835172	FXR1	Fragile X mental retardation-related protein 1 isoform c						0.012			2	−19.301
gi\|119703744	DSG1	Desmoglein 1 preproprotein	0.10			4	−9.424
gi\|62122917	FILA2	Filaggrin family member 2	0.11			3	−9.185
gi\|54607120	TRFL	Lactotransferrin precursor	0.12			5	−8.747
gi\|189458821	TGM3	Transglutaminase 3 precursor	0.18			2	−6.951
gi\|38348366	SBSN	Suprabasin						0.21			2	−6.925
gi\|4885165	CYTA	Cystatin A						0.22			2	−6.580
gi\|15187164	LACRT	Lacritin precursor	0.24			2	−5.876
gi\|170296790	A8CED1	Mesotrypsin isoform 1 preproprotein						0.25	6	−6.665
gi\|239755818	LOC100293351³	PREDICTED: hypothetical protein isoform 2	0.35			2	−4.275
gi\|221316620	CD123	Cell division cycle 12	0.38	3	−5.063
gi\|116686122	KIF4A	Kinesin family member 4						0.42	2	−4.187
gi\|4501889	ACTH	Actin, gamma 2 propeptide	0.44	85	−4.302
gi\|14327896	CCNB1	cyclin B1						0.48	2	−3.487
gi\|48762942	HIP1R	Huntingtin interacting protein-1-related						0.50	2	−3.304
gi\|155722990	SLC4A1AP	Kanadaptin						0.53	2	−3.018
gi\|50658084	BCAT2	Branched chain aminotransferase 2, mitochondrial	0.55	4	−3.200
gi\|47825361	NCRP1	Non-specific cytotoxic cell receptor protein 1 homolog	0.56			2	−2.346
gi\|4502951	CO3A1	Collagen type III alpha 1 preproprotein	0.57	5	−2.948
gi\|114796644	RCC1	Regulator of chromosome condensation 1 isoform a	0.58	3	−2.920
gi\|7705999	TMEM9	Transmembrane protein 9	0.58	2	−2.911
gi\|19882251	CYTN	Cystatin SN precursor	0.58			3	−2.238
gi\|154240704	TM192	Transmembrane protein 192	0.58			2	−2.210
gi\|82546824	FOXK1	Forkhead box K1	0.58	3	−2.866
gi\|190684694	UBP8	Ubiquitin specific peptidase 8						0.59	2	−2.567
gi\|221219053	DNAJC7	DnaJ (Hsp40) homolog, sub-family C, member 7 isoform 1	0.59	3	−2.795
gi\|7657655	TRAM1	Translocation associated membrane protein 1						0.63	3	−2.199
gi\|4557555	EGLN	Endoglin isoform 2 precursor	0.64	2	−2.420
gi\|46909600	ADA15	A disintegrin and metalloproteinase domain 15 isoform 6 preproprotein	0.64	3	−2.370
gi\|8393009	FFR	Chromosome 11 open reading frame2	0.64	2	−2.346
gi\|109255232	CE170	Centrosomal protein 170 kDa isoform gamma	0.65	2	−2.330
gi\|63176611	SLTM	SAFB-like transcription modulator isoform a						0.65	5	−2.051
gi\|5453958	PPP5	Protein phosphatase 5, catalytic subunit	0.66	3	−2.249
gi\|8922331	MGN2	Mago-nashi homolog B						0.66	4	−1.986
gi\|30061491	E41L1	Erythrocyte membrane protein band 4.1-like 1 isoform b	0.665	5	−2.178

¹Weighted H:L ratios, scaled to number of measured peptides in each sample, if detected in both Standard and Proteominer samples.

²Bolding indicates a significant z-score (95% confidence), either >1.960 or <−1.960.

³Gene removed from NCBI database.