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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Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 1302 to 1351 of 3206 in total
Rank
expected
description
measured
Hugo
final
1302 1.92792 TRANSLATION INITIATION FACTOR EIF-2B GAMMA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q9NR50] 0.473798 EIF2B3 0.245756048
1303 TRANSLATION INITIATION FACTOR EIF-2B EPSILON SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [SWISSPROT;Acc:Q13144] EIF2B5
1304 0.310798 RAD9 HOMOLOG; CELL CYCLE CHECKPOINT CONTROL PROTEIN; RAD9 HOMOLOG (S. POMBE). [RefSeq;Acc:NM_004584] 0.0763771 RAD9A 0.245745146
1305 0.108468 "PROLYL 4-HYDROXYLASE ALPHA-2 SUBUNIT PRECURSOR (EC 1.14.11.2) (4-PH ALPHA-2) (PROCOLLAGEN-PROLINE,2-OXOGLUTARATE-4-DIOXYGENASE ALPHA-2 SUBUNIT). [SWISSPROT;Acc:O15460]" 0.0266534 P4HA2 0.245725928
1306 0.136588 HYALURONAN BINDING PROTEIN 4; INTRACELLULAR ANTIGEN DETECTED BY MONOCLONAL ANTIBODY KI-1; INTRACELLULAR HYALURONAN-BINDING PROTEIN; CHROMODOMAIN HELICASE DNA BINDING PROTEIN 3 INTERACTING PROTEIN. [RefSeq;Acc:NM_014282] 0.0335632 HABP4 0.245725832
1307 0.58514 PROTEIN DISULFIDE ISOMERASE PRECURSOR (PDI) (EC 5.3.4.1) (PROLYL 4- HYDROXYLASE BETA SUBUNIT) (CELLULAR THYROID HORMONE BINDING PROTEIN) (P55). [SWISSPROT;Acc:P07237] 0.143784 P4HB 0.245725809
1308 3.55876 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 RAD1 0.245725477
1309 0.170682 HOMEOBOX PROSPERO-LIKE PROTEIN PROX1 (PROX 1). [SWISSPROT;Acc:Q92786] 0.0419409 PROX1 0.245725384
1310 0.818463 HUS1 CHECKPOINT PROTEIN; HUS1 (S. POMBE) CHECKPOINT HOMOLOG; HUS1+-LIKE PROTEIN. [RefSeq;Acc:NM_004507] 0.201117 HUS1 0.245725219
1311 0.170042 0.0417836 SERBP1 0.245725174
1312 0.170469 "3-HYDROXYANTHRANILATE 3,4-DIOXYGENASE (EC 1.13.11.6) (3-HAO) (3-HYDROXYANTHRANILIC ACID DIOXYGENASE) (3-HYDROXYANTHRANILATE OXYGENASE). [SWISSPROT;Acc:P46952]" 0.0418885 HAAO 0.245725029
1313 ZINC FINGER PROTEIN-LIKE 1; ZINC-FINGER PROTEIN IN MEN1 REGION. [RefSeq;Acc:NM_006782] ZFPL1
1314 0.135522 "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 P4HA1 0.245724679
1315 2.1077 HYDROXYACID OXIDASE 1 (EC 1.1.3.15) (HAOX1) (GLYCOLATE OXIDASE) (GOX). [SWISSPROT;Acc:Q9UJM8] 0.517862 HAO1 0.245700052
1316 1.82552 TGF BETA-INDUCIBLE NUCLEAR PROTEIN 1; HAIRY CELL LEUKEMIA PROTEIN 1. [RefSeq;Acc:NM_014886] 0.448528 no value 0.24569876
1317 2.10824 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 DDX54 0.245660361
1318 1.95163 0.479433 WDR74 0.245657732
1319 1.09872 0.269894 ARD1B 0.245644022
1320 0.100732 THIOREDOXIN DOMAIN-CONTAINING 2; SPERM-SPECIFIC THIOREDOXIN; THIOREDOXIN DOMAIN-CONTAINING 2 (SPERMATOZOA). [RefSeq;Acc:NM_032243] 0.0247366 TXNDC2 0.245568439
1321 0.121182 THIOREDOXIN (ATL-DERIVED FACTOR) (ADF) (SURFACE ASSOCIATED SULPHYDRYL PROTEIN) (SASP). [SWISSPROT;Acc:P10599] 0.0297584 TXN 0.245567824
1322 1.26602 60S ACIDIC RIBOSOMAL PROTEIN P1. [SWISSPROT;Acc:P05386] 0.310893 no value 0.245567211
1323 0.595639 CENTROMERE PROTEIN J; CENTROSOMAL P4.1-ASSOCIATED PROTEIN; LYST-INTERACTING PROTEIN LIP1; LAG-3-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_018451] 0.146257 CENPJ 0.24554638
1324 0.160458 "28S RIBOSOMAL PROTEIN S26, MITOCHONDRIAL PRECURSOR (MRP-S26) (MRP- S13). [SWISSPROT;Acc:Q9BYN8]" 0.0393961 MRPS26 0.245522816
1325 CHCHD4
1326 1.10704 ENHANCER OF RUDIMENTARY HOMOLOG. [SWISSPROT;Acc:Q14259] 0.271803 ERH 0.245522294
1327 3.37944 WD-REPEAT PROTEIN 12 (YTM1 HOMOLOG). [SWISSPROT;Acc:Q9GZL7] 0.829705 WDR12 0.245515529
1328 0.679841 NIF3-LIKE PROTEIN 1 (AMYOTROPHIC LATERAL SCLEROSIS 2 CHROMOSOMAL REGION CANDIDATE GENE PROTEIN 1) (MY018 PROTEIN) (MDS015). [SWISSPROT;Acc:Q9GZT8] 0.166892 no value 0.245486812
1329 1.14368 PROBABLE ATP-DEPENDENT 61 KDA NUCLEOLAR RNA HELICASE (DEAD-BOX PROTEIN 21). [SWISSPROT;Acc:Q9NY93] 0.280718 DDX56 0.245451525
1330 1.85732 SACCHAROMYCES CEREVISIAE NIP7P HOMOLOG. [RefSeq;Acc:NM_016101] 0.455858 NIP7 0.245438589
1331 0.867932 NNP-1 PROTEIN (NOVEL NUCLEAR PROTEIN 1) (NUCLEOLAR PROTEIN NOP52) (NOP52) (D21S2056E). [SWISSPROT;Acc:P56182] 0.213008 RRP1 0.245420148
1332 3.55541 NUCLEOLAR GTP-BINDING PROTEIN 1 (CHRONIC RENAL FAILURE GENE PROTEIN) (GTP-BINDING PROTEIN NGB). [SWISSPROT;Acc:Q9BZE4] 0.872438 GTPBP4 0.245383233
1333 0.419099 MYB-RELATED PROTEIN B (B-MYB). [SWISSPROT;Acc:P10244] 0.102811 MYBL2 0.245314353
1334 1.18321 AD24 PROTEIN. [RefSeq;Acc:NM_022451] 0.290237 NOC3L 0.24529627
1335 0.302799 SUPPRESSOR OF SWI4 1 HOMOLOG (SSF-1) (PETER PAN HOMOLOG). [SWISSPROT;Acc:Q9NQ55] 0.0742746 PPAN-P2RY11 0.245293412
1336 0.135226 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 CREBL1 0.245284191
1337 0.153273 DNA SEGMENT ON CHROMOSOME 6(UNIQUE) 2654 EXPRESSED SEQUENCE; DNA SEGMENT ON CHROMOSOME X (UNIQUE) 2654 EXPRESSED SEQUENCE. [RefSeq;Acc:NM_012135] 0.0375954 FAM50B 0.245283905
1338 0.142675 SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.0349958 SRPK2 0.245283336
1339 6.30537 GTP BINDING PROTEIN 2. [RefSeq;Acc:NM_019096] 1.5466 GTPBP2 0.245282989
1340 0.170257 SFRS PROTEIN KINASE 1; SR PROTEIN KINASE 1. [RefSeq;Acc:NM_003137] 0.0417611 SRPK1 0.24528272
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 0.674746 RAB3A INTERACTING PROTEIN ISOFORM ALPHA 1; RABIN3; SSX2 INTERACTING PROTEIN. [RefSeq;Acc:NM_022456] 0.165502 RAB3IP 0.245280446
1345 1.10693 PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [SWISSPROT;Acc:Q99848] 0.271421 EBNA1BP2 0.245201594
1346 0.804471 RAB3A INTERACTING PROTEIN (RABIN3)-LIKE 1. [RefSeq;Acc:NM_013401] 0.197255 RAB3IL1 0.245198397
1347 0.442236 WD REPEAT DOMAIN 26. [RefSeq;Acc:NM_025160] 0.108431 WDR26 0.24518809
1348 2.11039 J KAPPA-RECOMBINATION SIGNAL BINDING PROTEIN (RBP-J KAPPA). [SWISSPROT;Acc:Q06330] 0.517438 RBPJ 0.245185961
1349 0.163681 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER-BINDING PROTEIN 2 (HIV-EP2). [SWISSPROT;Acc:P31629] 0.0401322 HIVEP2 0.245185452
1350 0.192302 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 HIVEP1 0.245185177
1351 0.159829 HUMAN IMMUNODEFICIENCY VIRUS TYPE I ENHANCER BINDING PROTEIN 3. [RefSeq;Acc:NM_024503] 0.0391877 HIVEP3 0.245185167

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/