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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1308 to 1357 of 3206 in total
Rank
description
measured
expected
final
Hugo
1308 RAD1 HOMOLOG ISOFORM 1; EXONUCLEASE HOMOLOG RAD1; CELL CYCLE CHECKPOINT PROTEIN RAD1 A/B; RAD1-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN HRAD1; DNA REPAIR EXONUCLEASE (REC1); DNA REPAIR PROTEIN RAD1; RAD1-LIKE DNA DAMAGE CHECKPOINT PROTEIN. [RefS 0.874478 3.55876 0.245725477 RAD1
1309 HOMEOBOX PROSPERO-LIKE PROTEIN PROX1 (PROX 1). [SWISSPROT;Acc:Q92786] 0.0419409 0.170682 0.245725384 PROX1
1310 HUS1 CHECKPOINT PROTEIN; HUS1 (S. POMBE) CHECKPOINT HOMOLOG; HUS1+-LIKE PROTEIN. [RefSeq;Acc:NM_004507] 0.201117 0.818463 0.245725219 HUS1
1311 0.0417836 0.170042 0.245725174 SERBP1
1312 "3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [SWISSPROT;Acc:P46952]" 0.0418885 0.170469 0.245725029 HAAO
1313 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] ZFPL1
1314 "PROLYL 4-HYDROXYLASE ALPHA-1 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-1) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-1 SUBUNIT). [SWISSPROT;Acc:P13674]" 0.0333011 0.135522 0.245724679 P4HA1
1315 HYDROXYACID OXIDASE 1 (EC 1.1.3.15) (HAOX1) (GLYCOLATE OXIDASE) (GOX). [SWISSPROT;Acc:Q9UJM8] 0.517862 2.1077 0.245700052 HAO1
1316 TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 0.448528 1.82552 0.24569876 no value
1317 ATP-DEPENDENT RNA HELICASE MGC2835; ATP-DEPENDENT RNA HELICASE; APOPTOSIS RELATED PROTEIN APR-5; DEAD BOX HELICASE 97 KDA. [RefSeq;Acc:NM_024072] 0.517911 2.10824 0.245660361 DDX54
1318 0.479433 1.95163 0.245657732 WDR74
1319 0.269894 1.09872 0.245644022 ARD1B
1320 THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [RefSeq;Acc:NM_032243] 0.0247366 0.100732 0.245568439 TXNDC2
1321 THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599] 0.0297584 0.121182 0.245567824 TXN
1322 60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 0.310893 1.26602 0.245567211 no value
1323 CENTROMERE PROTEIN J; CENTROSOMAL P4.1-ASSOCIATED PROTEIN; LYST-INTERACTING PROTEIN LIP1; LAG-3-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018451] 0.146257 0.595639 0.24554638 CENPJ
1324 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" 0.0393961 0.160458 0.245522816 MRPS26
1325 CHCHD4
1326 ENHANCER OF RUDIMENTARY HOMOLOG. [SWISSPROT;Acc:Q14259] 0.271803 1.10704 0.245522294 ERH
1327 WD-REPEAT PROTEIN 12 (YTM1 HOMOLOG). [SWISSPROT;Acc:Q9GZL7] 0.829705 3.37944 0.245515529 WDR12
1328 NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [SWISSPROT;Acc:Q9GZT8] 0.166892 0.679841 0.245486812 no value
1329 PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [SWISSPROT;Acc:Q9NY93] 0.280718 1.14368 0.245451525 DDX56
1330 SACCHAROMYCES CEREVISIAE NIP7P HOMOLOG. [RefSeq;Acc:NM_016101] 0.455858 1.85732 0.245438589 NIP7
1331 NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [SWISSPROT;Acc:P56182] 0.213008 0.867932 0.245420148 RRP1
1332 NUCLEOLAR GTP-BINDING PROTEIN 1 (CHRONIC RENAL FAILURE GENE PROTEIN) (GTP-BINDING PROTEIN NGB). [SWISSPROT;Acc:Q9BZE4] 0.872438 3.55541 0.245383233 GTPBP4
1333 MYB-RELATED PROTEIN B (B-MYB). [SWISSPROT;Acc:P10244] 0.102811 0.419099 0.245314353 MYBL2
1334 AD24 PROTEIN. [RefSeq;Acc:NM_022451] 0.290237 1.18321 0.24529627 NOC3L
1335 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.0742746 0.302799 0.245293412 PPAN-P2RY11
1336 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 BETA (ACTIVATING TRANSCRIPTION FACTOR 6 BETA) (ATF6-BETA) (CAMP RESPONSIVE ELEMENT BINDING PROTEIN-LIKE 1) (CAMP RESPONSE ELEMENT BINDING PROTEIN-RELATED PROTEIN) (CREB-RP) (G13 PROTEIN). [SWISSPROT;A 0.0331688 0.135226 0.245284191 CREBL1
1337 DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [RefSeq;Acc:NM_012135] 0.0375954 0.153273 0.245283905 FAM50B
1338 SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.0349958 0.142675 0.245283336 SRPK2
1339 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] 1.5466 6.30537 0.245282989 GTPBP2
1340 SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [RefSeq;Acc:NM_003137] 0.0417611 0.170257 0.24528272 SRPK1
1341 XAP-5 PROTEIN (HXC-26 PROTEIN). [SWISSPROT;Acc:Q14320] FAM50A
1342 SERINE/THREONINE PROTEIN KINASE 23 (EC 2.7.1.37) (MUSCLE-SPECIFIC SERINE KINASE 1) (MSSK-1). [SWISSPROT;Acc:Q9UPE1] SRPK3
1343 CYCLIC-AMP-DEPENDENT TRANSCRIPTION FACTOR ATF-6 ALPHA (ACTIVATING TRANSCRIPTION FACTOR 6 ALPHA) (ATF6-ALPHA). [SWISSPROT;Acc:P18850] ATF6
1344 RAB3A INTERACTING PROTEIN ISOFORM ALPHA 1; RABIN3; SSX2 INTERACTING PROTEIN. [RefSeq;Acc:NM_022456] 0.165502 0.674746 0.245280446 RAB3IP
1345 PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [SWISSPROT;Acc:Q99848] 0.271421 1.10693 0.245201594 EBNA1BP2
1346 RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 0.197255 0.804471 0.245198397 RAB3IL1
1347 WD REPEAT DOMAIN 26. [RefSeq;Acc:NM_025160] 0.108431 0.442236 0.24518809 WDR26
1348 J KAPPA-RECOMBINATION SIGNAL BINDING PROTEIN (RBP-J KAPPA). [SWISSPROT;Acc:Q06330] 0.517438 2.11039 0.245185961 RBPJ
1349 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629] 0.0401322 0.163681 0.245185452 HIVEP2
1350 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] 0.0471496 0.192302 0.245185177 HIVEP1
1351 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] 0.0391877 0.159829 0.245185167 HIVEP3
1352 CCAAT-BOX-BINDING TRANSCRIPTION FACTOR (CCAAT-BINDING FACTOR) (CBF). [SWISSPROT;Acc:Q03701] 0.462442 1.88643 0.245141352 CEBPZ
1353 RING FINGER PROTEIN 20. [RefSeq;Acc:NM_019592] 0.188445 0.768755 0.245130113 RNF20
1354 RING FINGER PROTEIN 40; 95 KDA RETINOBLASTOMA PROTEIN BINDING PROTEIN; LIKELY ORTHOLOG OF RAT STARING. [RefSeq;Acc:NM_014771] RNF40
1355 0.0726736 0.296523 0.245085879 TTLL12
1356 ZINC-FINGER PROTEIN ZPR1 (ZINC FINGER PROTEIN 259). [SWISSPROT;Acc:O75312] ZNF259
1357 ELONGATION FACTOR 1-ALPHA 2 (EF-1-ALPHA-2) (ELONGATION FACTOR 1 A-2) (EEF1A-2) (STATIN S1). [SWISSPROT;Acc:Q05639] 0.145347 0.593047 0.245085128 EEF1A2

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/