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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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 2602 to 2651 of 3206 in total
expected
measured
Rank
Hugo
description
final
1.36939 0.35663 860 HNRPK HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K (HNRNP K) (DC-STRETCH BINDING PROTEIN) (CSBP) (TRANSFORMATION UPREGULATED NUCLEAR PROTEIN) (TUNP). [SWISSPROT;Acc:Q07244] 0.260429826
1.36954 0.313207 2093 OGDH "2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.2) (ALPHA-KETOGLUTARATE DEHYDROGENASE). [SWISSPROT;Acc:Q02218]" 0.228695036
1.37021 0.332106 1514 WDSOF1 0.242375986
1.37218 0.398804 320 TFIP11 TUFTELIN-INTERACTING PROTEIN 11 (HSPC006). [SWISSPROT;Acc:Q9UBB9] 0.290635339
1.37291 0.301597 2391 ATP5D "ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P30049]" 0.219677182
1.37608 0.336304 1393 ABCF3 0.244392768
1.37786 0.321507 1862 AARS ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS). [SWISSPROT;Acc:P49588] 0.23333793
1.37814 0.121467 3120 CSRP1 CYSTEINE-RICH PROTEIN 1 (CRP1) (CRP). [SWISSPROT;Acc:P21291] 0.08813836
1.38037 0.137954 3078 HOMER1 "HOMER, NEURONAL IMMEDIATE EARLY GENE, 1B. [RefSeq;Acc:NM_004272]" 0.099939871
1.38339 0.210608 2946 PSMA5 PROTEASOME SUBUNIT ALPHA TYPE 5 (EC 3.4.25.1) (PROTEASOME ZETA CHAIN) (MACROPAIN ZETA CHAIN) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX ZETA CHAIN). [SWISSPROT;Acc:P28066] 0.152240511
1.38457 0.363013 787 no value CBF1 INTERACTING COREPRESSOR. [RefSeq;Acc:NM_004882] 0.262184649
1.38684 0.347203 1139 KCTD10 MSTP028 PROTEIN. [RefSeq;Acc:NM_031954] 0.250355484
1.38936 0.354858 974 TLE4 TRANSDUCIN-LIKE ENHANCER PROTEIN 4. [SWISSPROT;Acc:Q04727] 0.255411125
1.39492 0.345758 1229 GIT2 ARF GTPASE-ACTIVATING PROTEIN GIT2 (G PROTEIN-COUPLED RECEPTOR KINASE- INTERACTOR 2). [SWISSPROT;Acc:Q14161] 0.247869412
1.39495 0.352414 1067 MEIS1 HOMEOBOX PROTEIN MEIS1. [SWISSPROT;Acc:O00470] 0.252635578
1.39578 0.458256 189 CCDC22 JM1 PROTEIN. [RefSeq;Acc:NM_014008] 0.328315351
1.39743 0.169636 3020 COPB2 COATOMER BETA' SUBUNIT (BETA'-COAT PROTEIN) (BETA'-COP) (P102). [SWISSPROT;Acc:P35606] 0.121391411
3021 COPZ1 COATOMER ZETA-1 SUBUNIT (ZETA-1 COAT PROTEIN) (ZETA-1 COP) (CGI-120) (HSPC181). [SWISSPROT;Acc:Q9Y3C3]
1.40271 0.803534 9 POLE4 DNA POLYMERASE EPSILON P12 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 4). [SWISSPROT;Acc:Q9NR33] 0.572843995
1.40331 0.357881 995 no value TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 0.255026331
1.40333 0.384939 486 ARF1 ADP-RIBOSYLATION FACTOR 1. [SWISSPROT;Acc:P32889] 0.274303977
1.40784 0.284553 2765 HSD17B4 ESTRADIOL 17 BETA-DEHYDROGENASE 4 (EC 1.1.1.62) (17-BETA-HSD 4) (17-BETA-HYDROXYSTEROID DEHYDROGENASE 4). [SWISSPROT;Acc:P51659] 0.202120269
1.40872 0.33278 1763 ATP6V0D2 "ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [RefSeq;Acc:NM_152565]" 0.236228633
1.40952 0.337407 1624 PRKAR2B CAMP-DEPENDENT PROTEIN KINASE TYPE II-BETA REGULATORY CHAIN. [SWISSPROT;Acc:P31323] 0.239377235
1.41191 0.314489 2269 DHODH "DIHYDROOROTATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.3.3.1) (DIHYDROOROTATE OXIDASE) (DHODEHASE) (FRAGMENT). [SWISSPROT;Acc:Q02127]" 0.222740118
1.41955 0.167012 3030 UBE2E4P UBIQUITIN-CONJUGATING ENZYME E2E 3; UBIQUITIN CARRIER PROTEIN; UBIQUITIN-PROTEIN LIGASE. [RefSeq;Acc:NM_006357] 0.117651368
1.42504 0.487065 167 KPNA4 IMPORTIN ALPHA-4 SUBUNIT (KARYOPHERIN ALPHA-4 SUBUNIT) (QIP1 PROTEIN). [SWISSPROT;Acc:O00629] 0.341790406
1.42639 0.586469 52 KNG1 KININOGEN PRECURSOR (ALPHA-2-THIOL PROTEINASE INHIBITOR) [CONTAINS: BRADYKININ]. [SWISSPROT;Acc:P01042] 0.411156135
1.42825 0.457984 206 JUND TRANSCRIPTION FACTOR JUN-D. [SWISSPROT;Acc:P17535] 0.320660949
1.42971 0.345751 1541 POLR2H "DNA-DIRECTED RNA POLYMERASES I, II, AND III 17.1 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8) (RPABC3). [SWISSPROT;Acc:P52434]" 0.241832959
1.43033 0.30514 2575 SLC5A5 SODIUM/IODIDE COTRANSPORTER (NA(+)/I(-) COTRANSPORTER) (SODIUM-IODIDE SYMPORTER) (NA+/I-SYMPORTER). [SWISSPROT;Acc:Q92911] 0.213335384
1.4315 0.316686 2332 TRIT1 TRNA ISOPENTENYLPYROPHOSPHATE TRANSFERASE. [RefSeq;Acc:NM_017646] 0.221226685
1.43405 0.348199 1488 LIN7B LIN-7 HOMOLOG B; LIN-7B PROTEIN; LIKELY ORTHOLOG OF MOUSE LIN-7B; MAMMALIAN LIN-7 PROTEIN 2; LIKELY ORHOLOG OF MOUSE LIN 7 HOMOLOG B (C. ELEGANS). [RefSeq;Acc:NM_022165] 0.242808131
1.43987 0.381101 721 no value DJ470L14.3 (NOVEL PROTEIN SIMILAR TO THE ARP2/3 PROTEIN COMPLEX SUBUNIT P21-ARC (ARC21)). [SPTREMBL;Acc:Q9H5B6] 0.264677367
1.44441 0.352259 1425 DCLK2 0.243877431
1.45239 0.354424 1405 FMR1 FRAGILE X MENTAL RETARDATION 1 PROTEIN (PROTEIN FMR-1) (FMRP). [SWISSPROT;Acc:Q06787] 0.244028119
1.45394 0.404169 409 FNBP1 "BA138E2.1.2 (FORMIN-BINDING PROTEIN 17 (FBP17), ISOFORM 2). [SPTREMBL;Acc:Q96LH6]" 0.277981897
1.45621 0.341137 1825 RFK 0.234263602
1.45734 0.322756 2329 DPH1 CANDIDATE TUMOR SUPPRESSOR IN OVARIAN CANCER 2. [RefSeq;Acc:NM_080822] 0.221469252
1.45917 0.393043 589 PGM2L1 0.269360664
1.46589 0.346601 1761 OSGEP O-SIALOGLYCOPROTEIN ENDOPEPTIDASE. [RefSeq;Acc:NM_017807] 0.236444072
1.46751 0.363365 1243 KCND2 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 2; VOLTAGE-SENSITIVE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.2. [RefSeq;Acc:NM_012281]" 0.24760649
1.47133 0.327115 2300 SNX1 SORTING NEXIN 1. [SWISSPROT;Acc:Q13596] 0.222326059
1.47327 0.334139 2179 ADSS ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [SWISSPROT;Acc:P30520] 0.226800926
1.4734 0.605547 64 FTHL17 FERRITIN HEAVY POLYPEPTIDE-LIKE 17. [SWISSPROT;Acc:Q9BXU8] 0.410986154
1.4749 0.35972 1424 KPNB1 IMPORTIN BETA-1 SUBUNIT (KARYOPHERIN BETA-1 SUBUNIT) (NUCLEAR FACTOR P97) (IMPORTIN 90). [SWISSPROT;Acc:Q14974] 0.243894501
1.47537 0.39546 647 no value RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 0.268041237
1.47582 0.337171 2096 STAM2 SIGNAL TRANSDUCING ADAPTOR MOLECULE 2; STAM-LIKE PROTEIN CONTAINING SH3 AND ITAM DOMAINS 2. [RefSeq;Acc:NM_005843] 0.228463498
1.47645 0.390781 729 ACTR2 ACTIN-LIKE PROTEIN 2 (ACTIN-RELATED PROTEIN 2). [SWISSPROT;Acc:O15142] 0.264676081
1.47667 0.352885 1649 COQ5 0.238973501

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/