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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank measured Gene description Hugo expected final
Results: HTML CSV LaTeX Showing element 1351 to 1400 of 3206 in total
Rank
measured
description
Hugo
expected
final
1351 0.0391877 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] HIVEP3 0.159829 0.245185167
1352 0.462442 CCAAT-BOX-BINDING TRANSCRIPTION FACTOR (CCAAT-BINDING FACTOR) (CBF). [SWISSPROT;Acc:Q03701] CEBPZ 1.88643 0.245141352
1353 0.188445 RING FINGER PROTEIN 20. [RefSeq;Acc:NM_019592] RNF20 0.768755 0.245130113
1354 RING FINGER PROTEIN 40; 95 KDA RETINOBLASTOMA PROTEIN BINDING PROTEIN; LIKELY ORTHOLOG OF RAT STARING. [RefSeq;Acc:NM_014771] RNF40
1355 0.0726736 TTLL12 0.296523 0.245085879
1356 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] ZNF259
1357 0.145347 ELONGATION FACTOR 1-ALPHA 2 (EF-1-ALPHA-2) (ELONGATION FACTOR 1 A-2) (EEF1A-2) (STATIN S1). [SWISSPROT;Acc:Q05639] EEF1A2 0.593047 0.245085128
1358 0.14659 ELONGATION FACTOR 1-ALPHA 1 (EF-1-ALPHA-1) (ELONGATION FACTOR 1 A-1) (EEF1A-1) (ELONGATION FACTOR TU) (EF-TU). [SWISSPROT;Acc:P04720] EEF1AL3 0.598119 0.245085008
1359 0.106233 MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] MYBL1 0.433454 0.24508483
1360 0.779006 PROTEASOME SUBUNIT BETA TYPE 5 PRECURSOR (EC 3.4.25.1) (PROTEASOME EPSILON CHAIN) (MACROPAIN EPSILON CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX EPSILON CHAIN) (PROTEASOME SUBUNIT X) (PROTEASOME CHAIN 6) (PROTEASOME SUBUNIT MB1). [SWISSPROT;Acc:P2 PSMB5 3.17883 0.245060604
1361 0.588043 TRANSLATION INITIATION FACTOR IF-2. [SWISSPROT;Acc:O60841] EIF5B 2.39991 0.245027105
1362 0.596229 no value 2.43411 0.244947435
1363 0.230116 ATP-DEPENDENT RNA HELICASE DDX24 (DEAD-BOX PROTEIN 24). [SWISSPROT;Acc:Q9GZR7] DDX24 0.939561 0.244918638
1364 0.0938754 HISTONE H2B.C (H2B/C). [SWISSPROT;Acc:Q99880] HIST1H2BL 0.38338 0.244862538
1365 0.0957148 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] no value 0.390892 0.24486252
1366 0.0836563 "TESTIS-SPECIFIC HISTONE H2B; H2B HISTONE FAMILY, MEMBER U, (TESTIS-SPECIFIC). [RefSeq;Acc:NM_170610]" HIST1H2BA 0.341646 0.244862519
1367 0.0942586 HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] no value 0.384945 0.244862513
1368 0.157068 HISTONE H3.1 (H3/A) (H3/C) (H3/D) (H3/F) (H3/H) (H3/I) (H3/J) (H3/K) (H3/L). [SWISSPROT;Acc:P16106] 0.641454 0.244862453
1369 0.0960725 HISTONE H2B.Q (H2B/Q) (H2B-GL105). [SWISSPROT;Acc:Q16778] HIST2H2BA 0.392353 0.244862407
1370 0.0946163 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] no value 0.386406 0.244862399
1371 0.0943097 HISTONE H2B. [RefSeq;Acc:NM_175055] 0.385154 0.244862315
1372 0.147768 HISTONE H3.4 (H3T) (H3/T) (H3/G). [SWISSPROT;Acc:Q16695] HIST3H3 0.603475 0.244861842
1373 0.403732 ARID4B 1.64923 0.244800301
1374 0.467786 MKI67 (FHA DOMAIN) INTERACTING NUCLEOLAR PHOSPHOPROTEIN; NUCLEOLAR PHOSPHOPROTEIN NOPP34; NUCLEOLAR PROTEIN INTERACTING WITH THE FHA DOMAIN OF PKI-67. [RefSeq;Acc:NM_032390] MKI67IP 1.91164 0.244704024
1375 1.02216 PROTEASOME SUBUNIT ALPHA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C3) (MACROPAIN SUBUNIT C3) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C3). [SWISSPROT;Acc:P25787] PSMA2 4.1775 0.244682226
1376 0.149037 C14orf129 0.609191 0.244647409
1377 0.18361 HOMEOBOX PROTEIN PRH (HEMATOPOIETICALLY EXPRESSED HOMEOBOX) (HOMEOBOX PROTEIN HEX). [SWISSPROT;Acc:Q03014] HHEX 0.750509 0.244647299
1378 0.034279 GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841] GSK3B 0.140116 0.244647292
1379 0.0439474 "SUPPRESSOR OF VAR1, 3-LIKE 1. [RefSeq;Acc:NM_003171]" SUPV3L1 0.179636 0.244646953
1380 0.200609 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] BAG1 0.819994 0.244646912
1381 0.0268629 GLYCOGEN SYNTHASE KINASE-3 ALPHA (EC 2.7.1.37) (GSK-3 ALPHA). [SWISSPROT;Acc:P49840] GSK3A 0.109803 0.244646321
1382 0.191835 DDX55 0.784198 0.24462572
1383 0.427194 ATAXIN-1 UBIQUITIN-LIKE INTERACTING PROTEIN. [RefSeq;Acc:NM_020131] UBQLN4 1.74675 0.244565049
1384 0.508151 UBIQUILIN 1 ISOFORM 1. [RefSeq;Acc:NM_013438] UBQLN1 2.0779 0.244550267
1385 0.28719 AUTOANTIGEN NGP-1. [SWISSPROT;Acc:Q13823] GNL2 1.17469 0.244481523
1386 0.037776 BA271B5.1 (SIMILAR TO RIBOSOMAL PROTEIN S7). [SPTREMBL;Acc:Q9H1S9] no value 0.154523 0.244468461
1387 0.0307397 APOLIPOPROTEIN B-100 PRECURSOR (APO B-100) [CONTAINS: APOLIPOPROTEIN B-48 (APO B-48)]. [SWISSPROT;Acc:P04114] APOB 0.125741 0.244468391
1388 0.038293 40S RIBOSOMAL PROTEIN S7 (S8). [SWISSPROT;Acc:P23821] RPS7 0.156638 0.244468137
1389 1.1639 26S PROTEASOME-ASSOCIATED PAD1 HOMOLOG. [RefSeq;Acc:NM_005805] PSMD14 4.76096 0.244467502
1390 0.410655 no value 1.68007 0.244427316
1391 0.131799 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3 [INCLUDES: PHOSPHORIBOSYLAMINE--GLYCINE LIGASE (EC 6.3.4.13) (GARS) (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) (PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE); PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (EC 6. GART 0.53927 0.244402618
1392 0.038432 WDR82 0.157255 0.244392865
1393 0.336304 ABCF3 1.37608 0.244392768
1394 0.240046 UBIQUITIN-CONJUGATING ENZYME E2 A (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE A) (UBIQUITIN CARRIER PROTEIN A) (HR6A) (HHR6A). [SWISSPROT;Acc:P49459] UBE2A 0.982761 0.244256742
1395 0.066057 MYOSIN VIIA. [SWISSPROT;Acc:Q13402] MYO7A 0.270441 0.244256603
1396 0.222353 UBIQUITIN-CONJUGATING ENZYME E2 B (EC 6.3.2.19) (UBIQUITIN-PROTEIN LIGASE B) (UBIQUITIN CARRIER PROTEIN B) (HR6B) (HHR6B) (E2-17 KDA). [SWISSPROT;Acc:P23567] UBE2B 0.910326 0.244256453
1397 0.361623 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 3 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT) (EIF-2-GAMMA). [SWISSPROT;Acc:P41091] EIF2S3 1.48057 0.244245797
1398 0.11514 MEGF6 (FRAGMENT). [SPTREMBL;Acc:O75095] MEGF6 0.471496 0.244201435
1399 0.0746708 LSG1 0.305803 0.244179423
1400 0.529846 PROTEASOME SUBUNIT ALPHA TYPE 4 (EC 3.4.25.1) (PROTEASOME COMPONENT C9) (MACROPAIN SUBUNIT C9) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C9) (PROTEASOME SUBUNIT L). [SWISSPROT;Acc:P25789] PSMA4 2.17049 0.244113541

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/