MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.

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description	Rank	Gene	expected	measured	final	Hugo

Results: HTML CSV LaTeX

Showing element 3158 to 3206 of 3206 in total

description	Rank	expected	measured	final	Hugo
WISKOTT-ALDRICH SYNDROME PROTEIN INTERACTING PROTEIN (WASP INTERACTING PROTEIN) (PRPL-2 PROTEIN). [SWISSPROT;Acc:O43516]	106	0.649898	0.23886	0.367534598	WIPF1
WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312]	1408	0.235798	0.0575359	0.244005038	WBP11
WW DOMAIN BINDING PROTEIN 2 (WBP-2). [SWISSPROT;Acc:Q969T9]	783	0.372839	0.0979343	0.262671823	WBP2
XAP-5 PROTEIN (HXC-26 PROTEIN). [SWISSPROT;Acc:Q14320]	1341	0.170257	0.0417611	0.24528272	FAM50A
XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736]	223	0.309963	0.0985042	0.317793414	XPR1
XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266]	11	1.5	0.813888	0.542592	XAB1
XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7]	451	1.59982	0.441621	0.27604418	XAB2
XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385]	2490	0.801332	0.172887	0.215749527	REXO4
XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108]	2228	1.33096	0.298587	0.224339574	XYLB
YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933]	1746	0.566199	0.134029	0.236717126	SEC31A
YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [RefSeq;Acc:NM_020470]	939	0.472359	0.121116	0.256406674	YIF1A
YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906]	2601	0.119307	0.0253936	0.212842499	VPS72
YME1-LIKE 1 ISOFORM 3; ATP-DEPENDENT METALLOPROTEASE FTSH1 HOMOLOG. [RefSeq;Acc:NM_014263]	171	2.19797	0.747794	0.340220294	YME1L1
Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24]	2154	0.151289	0.0343914	0.227322542	TMBIM4
ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3]	458	9.03714	2.49065	0.275601573	LDB3
ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315]	2457	0.125458	0.0271894	0.216721134	ZEB2
ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7]	2827	0.833576	0.161283	0.193483258	no value
ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697]	2828	0.821543	0.158934	0.19345792	ZNF174
ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022]	2826	0.84962	0.164415	0.193515925	ZNF18
ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7]	731	0.117755	0.0311669	0.26467581	ZMYM2
ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670]	1637	0.32156	0.0769103	0.239178691	ZNF207
ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771]	2818	0.8591	0.166266	0.193535095	ZNF213
ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58]	2825	0.849984	0.164486	0.193516584	ZNF215
ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5]	2820	0.857277	0.16591	0.193531379	ZNF232
ZINC FINGER PROTEIN 24 (ZINC FINGER PROTEIN 191) (ZINC FINGER PROTEIN KOX17) (RETINOIC ACID SUPPRESSION PROTEIN A) (RSG-A). [SWISSPROT;Acc:P17028]	2823	0.851807	0.164842	0.193520363	ZNF24
ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310]	720	0.119935	0.0317441	0.264677534	ZMYM6
ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202]	730	0.116875	0.030934	0.264675936	ZMYM3
ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095]	727	0.150694	0.0398851	0.264676099	ZMYM4
ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6]	2817	0.862746	0.166977	0.19354132	ZNF274
ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2]	2768	0.282946	0.0570468	0.20161727	no value
ZINC FINGER PROTEIN 288 (DENDRITIC-DERIVED BTB/POZ ZINC FINGER PROTEIN). [SWISSPROT;Acc:Q9HC78]	2806	0.513743	0.101567	0.197700017	ZBTB20
ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12]	1961	0.0842001	0.0194686	0.231218253	SCAPER
ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309]	2821	0.856912	0.165839	0.193530958	ZSCAN12
ZINC FINGER PROTEIN 40 (HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER- BINDING PROTEIN 1) (HIV-EP1) (MAJOR HISTOCOMPATIBILITY COMPLEX BINDING PROTEIN 1) (MBP-1) (POSITIVE REGULATORY DOMAIN II BINDING FACTOR 1) (PRDII-BF1). [SWISSPROT;Acc:P15822]	1350	0.192302	0.0471496	0.245185177	HIVEP1
ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337]	2816	1.1643	0.225841	0.193971485	ZNF444
ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164]	2819	0.858735	0.166195	0.193534676	ZNF394
ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151]	2356	0.115399	0.0254221	0.220297403	GLI1
ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070]	2357				GLI2
ZINC FINGER PROTEIN GLI3. [SWISSPROT;Acc:P10071]	2360	0.0927234	0.0204267	0.220297142	GLI3
ZINC FINGER PROTEIN SLUG (NEURAL CREST TRANSCRIPTION FACTOR SLUG) (SNAIL HOMOLOG 2). [SWISSPROT;Acc:O43623]	735	0.328537	0.0869475	0.264650557	SNAI2
ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488]	1205	0.525788	0.130571	0.248333929	ZNF593
ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915]	603	1.01187	0.272286	0.269091879	ZIC1
ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409]	599	1.14212	0.307359	0.269112703	ZIC2
ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481]	600	0.932647	0.25098	0.269105031	ZIC3
ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1]	613	0.337014	0.0906044	0.268844618	ZIC4
ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782]	1313	0.170469	0.0418885	0.245725029	ZFPL1
ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414]	1288	0.192307	0.0473076	0.246000406	ZNF622
ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312]	1356	0.296523	0.0726736	0.245085879	ZNF259
ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543]	1503	0.112006	0.0271819	0.242682535	ZRF1

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots