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 expected measured final Rank description Hugo
Results: HTML CSV LaTeX Showing element 1358 to 1407 of 3206 in total
expected
measured
final
Rank
description
Hugo
0.427993 0.0966308 0.22577659 2201 NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [SWISSPROT;Acc:P00387] CYB5R3
0.428154 0.119541 0.279200942 375 "DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]" DYNC1I2
0.428402 0.0771117 0.179998459 2886 MUSCLE-SPECIFIC BETA 1 INTEGRIN BINDING PROTEIN. [RefSeq;Acc:NM_014446] ITGB1BP3
0.428531 0.252763 0.589835975 7 ADIPONECTIN RECEPTOR 2. [RefSeq;Acc:NM_024551] ADIPOR2
0.428577 0.0892656 0.208283692 2689 EH-DOMAIN CONTAINING PROTEIN 2. [SWISSPROT;Acc:Q9NZN4] EHD2
0.428605 0.0811667 0.189374132 2858 "TREHALASE PRECURSOR (EC 3.2.1.28) (ALPHA,ALPHA-TREHALASE) (ALPHA,ALPHA-TREHALOSE GLUCOHYDROLASE). [SWISSPROT;Acc:O43280]" TREH
0.428734 0.0897053 0.209232998 2672 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] no value
0.429323 0.0933761 0.217496151 2430 SIPL PROTEIN. [RefSeq;Acc:NM_018269] ADI1
0.430463 0.115475 0.268257667 637 CYTOCHROME P450 4F3 (EC 1.14.13.30) (CYPIVF3) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:Q08477] CYP4F3
0.431206 0.155731 0.36115221 115 BRG1-BINDING PROTEIN ELD/OSA1; ELD (EYELID)/OSA PROTEIN. [RefSeq;Acc:NM_020732] ARID1B
0.431998 0.097609 0.225947805 2196 TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [SWISSPROT;Acc:Q13625] TP53BP2
0.432185 0.107333 0.248349665 1201 FAM40A
0.43244 0.101148 0.233900657 1833 N-ACETYLTRANSFERASE 5 (EC 2.3.1.-). [SWISSPROT;Acc:Q9Y6D2] NAT5
0.43247 0.108251 0.250308692 1141 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" SMARCB1
0.432472 0.116014 0.268257829 636 "DJ18D14.4 (CYTOCHROME P450, SUBFAMILY IVA, POLYPEPTIDE 11). [SPTREMBL;Acc:Q9NTL5]" CYP4A22
0.432583 0.11358 0.262562329 785 BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [SWISSPROT;Acc:P38398] BRCA1
0.432823 0.116093 0.268222807 639 C18orf55
0.433454 0.106233 0.24508483 1359 MYB-RELATED PROTEIN A (A-MYB). [SWISSPROT;Acc:P10243] MYBL1
0.434244 0.107742 0.248113964 1208 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] NOVA1
0.43488 0.105382 0.242324319 1525 KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [SWISSPROT;Acc:O15066] KIF3B
0.43497 0.116815 0.268558751 619 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671] OCA2
0.437464 0.115708 0.264497193 750 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 6 INTERACTING PROTEIN (HSPC021/HSPC025). [SWISSPROT;Acc:Q9Y262] EIF3EIP
0.437657 0.098654 0.225413966 2207 SLC47A2
0.438523 0.103336 0.235645565 1776 WDR70
0.440396 0.102272 0.232227359 1905 "UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2) (RIESKE IRON-SULFUR PROTEIN) (RISP). [SWISSPROT;Acc:P47985]" UQCRFSL1
0.440965 0.110645 0.250915606 1106 C2orf25
0.441415 0.124527 0.282108673 353 TRANSCRIPTION INITIATION FACTOR TFIID 55 KDA SUBUNIT (TAFII-55) (TAFII55). [SWISSPROT;Acc:Q15545] TAF7
0.442236 0.108431 0.24518809 1347 WD REPEAT DOMAIN 26. [RefSeq;Acc:NM_025160] WDR26
0.442453 0.166283 0.375820709 97 POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY A MEMBER 4 (POTASSIUM CHANNEL KV1.4) (HK1) (HPCN2) (HBK4) (HUKII). [SWISSPROT;Acc:P22459] KCNA4
0.442554 0.117061 0.264512353 739 PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9] CROT
0.442722 0.108852 0.245869869 1297 UPRT
0.44293 0.123465 0.278746077 390 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 SMARCD3
0.443397 0.118945 0.268258468 630 CYTOCHROME P450 4F2 (EC 1.14.13.30) (CYPIVF2) (LEUKOTRIENE-B4 OMEGA- HYDROXYLASE) (LEUKOTRIENE-B4 20-MONOOXYGENASE) (CYTOCHROME P450- LTB-OMEGA). [SWISSPROT;Acc:P78329] CYP4F2
631 CYTOCHROME P450 4F8 (EC 1.14.14.1) (CYPIVF8). [SWISSPROT;Acc:P98187] CYP4F8
632 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] CYP4A11
0.443579 0.110079 0.248160981 1207 no value
0.443899 0.11908 0.268259221 624 FLOTILLIN-1. [SWISSPROT;Acc:O75955] FLOT1
0.444481 0.0444208 0.09993858 3079 PLASMA CARBOXYPEPTIDASE B2 ISOFORM A PREPROPROTEIN; CARBOXYPEPTIDASE U; THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR; CARBOXYPEPTIDASE B-LIKE PROTEIN; THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR. [RefSeq;Acc:NM_001872] CPB2
0.444789 0.187173 0.420813015 41 CCAAT DISPLACEMENT PROTEIN (CDP) (CUT-LIKE 1). [SWISSPROT;Acc:P39880] CUTL1
0.445662 0.110103 0.247054943 1263 C9orf7
0.44632 0.11907 0.266781681 669 RSRC2
0.446911 0.0926594 0.207333004 2718 ABHD14A
0.447876 0.118199 0.2639101 757 FAS APOPTOTIC INHIBITORY MOLECULE. [RefSeq;Acc:NM_018147] FAIM
0.44823 0.114475 0.255393436 976 60S ACIDIC RIBOSOMAL PROTEIN P2. [SWISSPROT;Acc:P05387] RPLP2
0.449228 0.109553 0.243869483 1426 MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [SWISSPROT;Acc:Q15691] MAPRE1
1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] SLC39A7
0.450013 0.0937258 0.208273539 2690 SIN3 ASSOCIATED POLYPEPTIDE P18 (2HOR0202). [SWISSPROT;Acc:O00422] SAP18
0.450503 0.117829 0.261549868 810 no value
0.450566 0.122154 0.271112334 536 BROMODOMAIN-CONTAINING PROTEIN 3 (RING3-LIKE PROTEIN). [SWISSPROT;Acc:Q15059] BRD3
0.450769 0.10685 0.23703937 1725 VPS25

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/