Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 measured expected Hugo final
Results: HTML CSV LaTeX Showing element 3158 to 3206 of 3206 in total
description
Rank
measured
expected
Hugo
final
WISKOTT-ALDRICH SYNDROME PROTEIN INTERACTING PROTEIN (WASP INTERACTING PROTEIN) (PRPL-2 PROTEIN). [SWISSPROT;Acc:O43516] 106 0.23886 0.649898 WIPF1 0.367534598
WW DOMAIN BINDING PROTEIN 11; NPW38-BINDING PROTEIN NPWBP; SH3 DOMAIN-BINDING PROTEIN SNP70. [RefSeq;Acc:NM_016312] 1408 0.0575359 0.235798 WBP11 0.244005038
WW DOMAIN BINDING PROTEIN 2 (WBP-2). [SWISSPROT;Acc:Q969T9] 783 0.0979343 0.372839 WBP2 0.262671823
XAP-5 PROTEIN (HXC-26 PROTEIN). [SWISSPROT;Acc:Q14320] 1341 0.0417611 0.170257 FAM50A 0.24528272
XENOTROPIC AND POLYTROPIC RETROVIRUS RECEPTOR. [RefSeq;Acc:NM_004736] 223 0.0985042 0.309963 XPR1 0.317793414
XPA BINDING PROTEIN 1; MBD2 INTERACTOR PROTEIN; PUTATIVE ATP(GTP)-BINDING PROTEIN. [RefSeq;Acc:NM_007266] 11 0.813888 1.5 XAB1 0.542592
XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] 451 0.441621 1.59982 XAB2 0.27604418
XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [RefSeq;Acc:NM_020385] 2490 0.172887 0.801332 REXO4 0.215749527
XYLULOKINASE HOMOLOG; XYLULOKINASE (H. INFLUENZAE) HOMOLOG. [RefSeq;Acc:NM_005108] 2228 0.298587 1.33096 XYLB 0.224339574
YEAST SEC31P HOMOLOG. [RefSeq;Acc:NM_014933] 1746 0.134029 0.566199 SEC31A 0.236717126
YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [RefSeq;Acc:NM_020470] 939 0.121116 0.472359 YIF1A 0.256406674
YL-1 PROTEIN (TRANSCRIPTION FACTOR-LIKE 1). [SWISSPROT;Acc:Q15906] 2601 0.0253936 0.119307 VPS72 0.212842499
YME1-LIKE 1 ISOFORM 3; ATP-DEPENDENT METALLOPROTEASE FTSH1 HOMOLOG. [RefSeq;Acc:NM_014263] 171 0.747794 2.19797 YME1L1 0.340220294
Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [SWISSPROT;Acc:Q9HC24] 2154 0.0343914 0.151289 TMBIM4 0.227322542
ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] 458 2.49065 9.03714 LDB3 0.275601573
ZINC FINGER HOMEOBOX PROTEIN 1B (SMAD INTERACTING PROTEIN 1) (SMADIP1) (HRIHFB2411). [SWISSPROT;Acc:O60315] 2457 0.0271894 0.125458 ZEB2 0.216721134
ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 2827 0.161283 0.833576 no value 0.193483258
ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697] 2828 0.158934 0.821543 ZNF174 0.19345792
ZINC FINGER PROTEIN 18 (ZINC FINGER PROTEIN KOX11) (FRAGMENT). [SWISSPROT;Acc:P17022] 2826 0.164415 0.84962 ZNF18 0.193515925
ZINC FINGER PROTEIN 198 (FUSED IN MYELOPROLIFERATIVE DISORDERS PROTEIN) (REARRANGED IN ATYPICAL MYELOPROLIFERATIVE DISORDER PROTEIN). [SWISSPROT;Acc:Q9UBW7] 731 0.0311669 0.117755 ZMYM2 0.26467581
ZINC FINGER PROTEIN 207. [SWISSPROT;Acc:O43670] 1637 0.0769103 0.32156 ZNF207 0.239178691
ZINC FINGER PROTEIN 213 (PUTATIVE TRANSCRIPTION FACTOR CR53). [SWISSPROT;Acc:O14771] 2818 0.166266 0.8591 ZNF213 0.193535095
ZINC FINGER PROTEIN 215 (BWSCR2 ASSOCIATED ZINC-FINGER PROTEIN 2) (BAZ 2). [SWISSPROT;Acc:Q9UL58] 2825 0.164486 0.849984 ZNF215 0.193516584
ZINC FINGER PROTEIN 232. [SWISSPROT;Acc:Q9UNY5] 2820 0.16591 0.857277 ZNF232 0.193531379
ZINC FINGER PROTEIN 24 (ZINC FINGER PROTEIN 191) (ZINC FINGER PROTEIN KOX17) (RETINOIC ACID SUPPRESSION PROTEIN A) (RSG-A). [SWISSPROT;Acc:P17028] 2823 0.164842 0.851807 ZNF24 0.193520363
ZINC FINGER PROTEIN 258. [RefSeq;Acc:NM_145310] 720 0.0317441 0.119935 ZMYM6 0.264677534
ZINC FINGER PROTEIN 261 (DXS6673E PROTEIN). [SWISSPROT;Acc:Q14202] 730 0.030934 0.116875 ZMYM3 0.264675936
ZINC FINGER PROTEIN 262; CELL DEATH INHIBITING RNA. [RefSeq;Acc:NM_005095] 727 0.0398851 0.150694 ZMYM4 0.264676099
ZINC FINGER PROTEIN 274 (ZINC FINGER PROTEIN SP2114) (ZINC FINGER PROTEIN HFB101) (ZINC FINGER PROTEIN ZFP2) (ZF2). [SWISSPROT;Acc:Q96GC6] 2817 0.166977 0.862746 ZNF274 0.19354132
ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 2768 0.0570468 0.282946 no value 0.20161727
ZINC FINGER PROTEIN 288 (DENDRITIC-DERIVED BTB/POZ ZINC FINGER PROTEIN). [SWISSPROT;Acc:Q9HC78] 2806 0.101567 0.513743 ZBTB20 0.197700017
ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] 1961 0.0194686 0.0842001 SCAPER 0.231218253
ZINC FINGER PROTEIN 305. [SWISSPROT;Acc:O43309] 2821 0.165839 0.856912 ZSCAN12 0.193530958
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 0.0471496 0.192302 HIVEP1 0.245185177
ZINC FINGER PROTEIN 444; ENDOTHELIAL ZINC FINGER PROTEIN 2. [RefSeq;Acc:NM_018337] 2816 0.225841 1.1643 ZNF444 0.193971485
ZINC FINGER PROTEIN 99. [RefSeq;Acc:NM_032164] 2819 0.166195 0.858735 ZNF394 0.193534676
ZINC FINGER PROTEIN GLI1 (GLIOMA-ASSOCIATED ONCOGENE) (ONCOGENE GLI). [SWISSPROT;Acc:P08151] 2356 0.0254221 0.115399 GLI1 0.220297403
ZINC FINGER PROTEIN GLI2 (TAX HELPER PROTEIN). [SWISSPROT;Acc:P10070] 2357 GLI2
ZINC FINGER PROTEIN GLI3. [SWISSPROT;Acc:P10071] 2360 0.0204267 0.0927234 GLI3 0.220297142
ZINC FINGER PROTEIN SLUG (NEURAL CREST TRANSCRIPTION FACTOR SLUG) (SNAIL HOMOLOG 2). [SWISSPROT;Acc:O43623] 735 0.0869475 0.328537 SNAI2 0.264650557
ZINC FINGER PROTEIN T86. [SWISSPROT;Acc:O00488] 1205 0.130571 0.525788 ZNF593 0.248333929
ZINC FINGER PROTEIN ZIC 1 (ZINC FINGER PROTEIN OF THE CEREBELLUM 1). [SWISSPROT;Acc:Q15915] 603 0.272286 1.01187 ZIC1 0.269091879
ZINC FINGER PROTEIN ZIC 2 (ZINC FINGER PROTEIN OF THE CEREBELLUM 2). [SWISSPROT;Acc:O95409] 599 0.307359 1.14212 ZIC2 0.269112703
ZINC FINGER PROTEIN ZIC 3 (ZINC FINGER PROTEIN OF THE CEREBELLUM 3). [SWISSPROT;Acc:O60481] 600 0.25098 0.932647 ZIC3 0.269105031
ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] 613 0.0906044 0.337014 ZIC4 0.268844618
ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] 1313 0.0418885 0.170469 ZFPL1 0.245725029
ZINC FINGER-LIKE PROTEIN 9. [RefSeq;Acc:NM_033414] 1288 0.0473076 0.192307 ZNF622 0.246000406
ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] 1356 0.0726736 0.296523 ZNF259 0.245085879
ZUOTIN RELATED FACTOR-1 (M-PHASE PHOSPHOPROTEIN 11). [SWISSPROT;Acc:Q99543] 1503 0.0271819 0.112006 ZRF1 0.242682535

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
- http://analysis.yellowcouch.org/