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

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/