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:
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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 1352 to 1401 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.423859 0.0446932 3058 GNAT2 "GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-2 SUBUNIT (TRANSDUCIN ALPHA-2 CHAIN). [SWISSPROT;Acc:P19087]" 0.105443556
0.42621 0.087666 2730 CCBL2 0.205687337
0.427267 0.0744051 2910 RRN3 RNA POLYMERASE I TRANSCRIPTION FACTOR RRN3. [RefSeq;Acc:NM_018427] 0.17414193
0.427411 0.102962 1576 RBKS RIBOKINASE (EC 2.7.1.15). [SWISSPROT;Acc:Q9H477] 0.240896935
0.427723 0.0979801 2079 no value LIM DOMAIN BINDING 1; CARBOXY TERMINAL LIM DOMAIN PROTEIN 2; LIM DOMAIN-BINDING FACTOR-1. [RefSeq;Acc:NM_003893] 0.229073723
0.427882 0.0898392 2644 TUB TUBBY PROTEIN HOMOLOG. [SWISSPROT;Acc:P50607] 0.20996256
0.427993 0.0966308 2201 CYB5R3 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] 0.22577659
0.428154 0.119541 375 DYNC1I2 "DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]" 0.279200942
0.428402 0.0771117 2886 ITGB1BP3 MUSCLE-SPECIFIC BETA 1 INTEGRIN BINDING PROTEIN. [RefSeq;Acc:NM_014446] 0.179998459
0.428531 0.252763 7 ADIPOR2 ADIPONECTIN RECEPTOR 2. [RefSeq;Acc:NM_024551] 0.589835975
0.428577 0.0892656 2689 EHD2 EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] 0.208283692
0.428605 0.0811667 2858 TREH "TREHALASE PRECURSOR (EC 3.2.1.28) (ALPHA,ALPHA-TREHALASE) (ALPHA,ALPHA-TREHALOSE GLUCOHYDROLASE). [SWISSPROT;Acc:O43280]" 0.189374132
0.428734 0.0897053 2672 no value TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 0.209232998
0.429323 0.0933761 2430 ADI1 SIPL PROTEIN. [RefSeq;Acc:NM_018269] 0.217496151
0.430463 0.115475 637 CYP4F3 CYTOCHROME P450 4F3 (EC 1.14.13.30) (CYPIVF3) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:Q08477] 0.268257667
0.431206 0.155731 115 ARID1B BRG1-BINDING PROTEIN ELD/OSA1; ELD (EYELID)/OSA PROTEIN. [RefSeq;Acc:NM_020732] 0.36115221
0.431998 0.097609 2196 TP53BP2 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] 0.225947805
0.432185 0.107333 1201 FAM40A 0.248349665
0.43244 0.101148 1833 NAT5 N-ACETYLTRANSFERASE 5 (EC 2.3.1.-). [SWISSPROT;Acc:Q9Y6D2] 0.233900657
0.43247 0.108251 1141 SMARCB1 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 0.250308692
0.432472 0.116014 636 CYP4A22 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" 0.268257829
0.432583 0.11358 785 BRCA1 BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [SWISSPROT;Acc:P38398] 0.262562329
0.432823 0.116093 639 C18orf55 0.268222807
0.433454 0.106233 1359 MYBL1 MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] 0.24508483
0.434244 0.107742 1208 NOVA1 RNA-BINDING PROTEIN NOVA-1 (NEURO-ONCOLOGICAL VENTRAL ANTIGEN 1) (ONCONEURAL VENTRAL ANTIGEN-1) (PARANEOPLASTIC RI ANTIGEN) (VENTRAL NEURON-SPECIFIC PROTEIN 1). [SWISSPROT;Acc:P51513] 0.248113964
0.43488 0.105382 1525 KIF3B KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [SWISSPROT;Acc:O15066] 0.242324319
0.43497 0.116815 619 OCA2 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] 0.268558751
0.437464 0.115708 750 EIF3EIP EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 INTERACTING PROTEIN (HSPC021/HSPC025). [SWISSPROT;Acc:Q9Y262] 0.264497193
0.437657 0.098654 2207 SLC47A2 0.225413966
0.438523 0.103336 1776 WDR70 0.235645565
0.440396 0.102272 1905 UQCRFSL1 "UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" 0.232227359
0.440965 0.110645 1106 C2orf25 0.250915606
0.441415 0.124527 353 TAF7 TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT (TAFII-55) (TAFII55). [SWISSPROT;Acc:Q15545] 0.282108673
0.442236 0.108431 1347 WDR26 WD REPEAT DOMAIN 26. [RefSeq;Acc:NM_025160] 0.24518809
0.442453 0.166283 97 KCNA4 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 4 (POTASSIUM CHANNEL KV1.4) (HK1) (HPCN2) (HBK4) (HUKII). [SWISSPROT;Acc:P22459] 0.375820709
0.442554 0.117061 739 CROT PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] 0.264512353
0.442722 0.108852 1297 UPRT 0.245869869
0.44293 0.123465 390 SMARCD3 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D3; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60C; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60C SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT C. [Sour 0.278746077
0.443397 0.118945 630 CYP4F2 CYTOCHROME P450 4F2 (EC 1.14.13.30) (CYPIVF2) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:P78329] 0.268258468
631 CYP4F8 CYTOCHROME P450 4F8 (EC 1.14.14.1) (CYPIVF8). [SWISSPROT;Acc:P98187]
632 CYP4A11 CYTOCHROME P450 4A11 PRECURSOR (EC 1.14.15.3) (CYPIVA11) (FATTY ACID OMEGA-HYDROXYLASE) (P-450 HK OMEGA) (LAURIC ACID OMEGA-HYDROXYLASE) (CYP4AII) (P450-HL-OMEGA). [SWISSPROT;Acc:Q02928]
0.443579 0.110079 1207 no value 0.248160981
0.443899 0.11908 624 FLOT1 FLOTILLIN-1. [SWISSPROT;Acc:O75955] 0.268259221
0.444481 0.0444208 3079 CPB2 PLASMA CARBOXYPEPTIDASE B2 ISOFORM A PREPROPROTEIN; CARBOXYPEPTIDASE U; THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR; CARBOXYPEPTIDASE B-LIKE PROTEIN; THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR. [RefSeq;Acc:NM_001872] 0.09993858
0.444789 0.187173 41 CUTL1 CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [SWISSPROT;Acc:P39880] 0.420813015
0.445662 0.110103 1263 C9orf7 0.247054943
0.44632 0.11907 669 RSRC2 0.266781681
0.446911 0.0926594 2718 ABHD14A 0.207333004
0.447876 0.118199 757 FAIM FAS APOPTOTIC INHIBITORY MOLECULE. [RefSeq;Acc:NM_018147] 0.2639101
0.44823 0.114475 976 RPLP2 60S ACIDIC RIBOSOMAL PROTEIN P2. [SWISSPROT;Acc:P05387] 0.255393436

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/