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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measured Hugo Gene Rank expected final description
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 3206 in total
measured
Hugo
Rank
expected
final
description
0.116077 U2AF1 1434 0.476394 0.243657561 SPLICING FACTOR U2AF 35 KDA SUBUNIT (U2 AUXILIARY FACTOR 35 KDA SUBUNIT) (U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT). [SWISSPROT;Acc:Q01081]
0.116081 no value 3109 1.26306 0.091904581 "MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE IB (EC 3.2.1.113) (PROCESSING ALPHA-1,2-MANNOSIDASE IB) (ALPHA-1,2-MANNOSIDASE IB) (MANNOSIDASE ALPHA CLASS 1A MEMBER 2). [SWISSPROT;Acc:O60476]"
0.116093 C18orf55 639 0.432823 0.268222807
0.116127 MXD1 194 0.359971 0.322600987 MAD PROTEIN (MAX DIMERIZER). [SWISSPROT;Acc:Q05195]
0.116337 CANT1 2783 0.580323 0.200469394 CA2+-DEPENDENT ENDOPLASMIC RETICULUM NUCLEOSIDE DIPHOSPHATASE; APYRASE; SOLUBLE CALCIUM-ACTIVATED NUCLEOTIDASE SCAN-1. [RefSeq;Acc:NM_138793]
0.116403 no value 2032 0.505621 0.23021789
0.116413 C7orf20 2444 0.536227 0.217096491
0.116452 ADRM1 1125 0.464548 0.250678078 ADHESION REGULATING MOLECULE 1 PRECURSOR (110 KDA CELL MEMBRANE GLYCOPROTEIN) (GP110). [SWISSPROT;Acc:Q16186]
0.116454 CDC73 1118 0.464305 0.250813582 PARAFIBROMIN. [RefSeq;Acc:NM_024529]
0.116498 PAF1 1117 0.464479 0.250814353
0.116797 SEPT6 3008 0.952641 0.122603373 SEPTIN 6. [SWISSPROT;Acc:Q14141]
0.116815 OCA2 619 0.43497 0.268558751 P PROTEIN (MELANOCYTE-SPECIFIC TRANSPORTER PROTEIN). [SWISSPROT;Acc:Q04671]
0.116856 BUB1B 1132 0.466478 0.250506991 MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA (EC 2.7.1.-) (HBUBR1) (MAD3/BUB1-RELATED PROTEIN KINASE) (MITOTIC CHECKPOINT KINASE MAD3L). [SWISSPROT;Acc:O60566]
0.116954 MAPKBP1 350 0.41404 0.282470293
0.117061 CROT 739 0.442554 0.264512353 PEROXISOMAL CARNITINE OCTANOYLTRANSFERASE (EC 2.3.1.-) (COT). [SWISSPROT;Acc:Q9UKG9]
0.117156 HNF4G 46 0.280936 0.417020247 HEPATOCYTE NUCLEAR FACTOR 4-GAMMA (HNF-4-GAMMA). [SWISSPROT;Acc:Q14541]
0.117195 SHROOM2 88 0.30421 0.385243746 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796]
0.117296 MLH3 2230 0.522903 0.224316938 DNA MISMATCH REPAIR PROTEIN MLH3 (MUTL PROTEIN HOMOLOG 3). [SWISSPROT;Acc:Q9UHC1]
0.117485 EGFL7 3124 1.55221 0.075688857 "EGF-LIKE-DOMAIN, MULTIPLE 7; NEU1 PROTEIN. [RefSeq;Acc:NM_016215]"
0.117541 NARS 2752 0.576375 0.203931468 "ASPARAGINYL-TRNA SYNTHETASE, CYTOPLASMIC (EC 6.1.1.22) (ASPARAGINE-- TRNA LIGASE) (ASNRS). [SWISSPROT;Acc:O43776]"
NARS2 2751
0.117602 EXOC6B 355 0.417668 0.281568135 EXOCYST COMPLEX COMPONENT SEC15B. [SWISSPROT;Acc:Q9Y2D4]
0.117727 GSPT1 973 0.460892 0.255432943 G1 TO S PHASE TRANSITION PROTEIN 1 HOMOLOG (GTP-BINDING PROTEIN GST1-HS). [SWISSPROT;Acc:P15170]
0.11779 RPLP0 1249 0.476127 0.247391977 60S ACIDIC RIBOSOMAL PROTEIN P0 (L10E). [SWISSPROT;Acc:P05388]
0.117829 no value 810 0.450503 0.261549868
0.117844 LIMS2 2514 0.548706 0.214767107 LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 2; ILK-BINDING PROTEIN. [RefSeq;Acc:NM_017980]
0.117871 NUP93 2925 0.704322 0.167353852
0.11794 PRSS12 2263 0.528749 0.223054795 NEUROTRYPSIN PRECURSOR (EC 3.4.21.-) (MOTOPSIN) (LEYDIN). [SWISSPROT;Acc:P56730]
0.118014 SEPT8 3023 0.986632 0.119612986 SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599]
0.118199 FAIM 757 0.447876 0.2639101 FAS APOPTOTIC INHIBITORY MOLECULE. [RefSeq;Acc:NM_018147]
0.118202 PRUNE 1659 0.494902 0.238839205 TCD37 HOMOLOG; PRUNE. [RefSeq;Acc:NM_021222]
0.11844 TOMM70A 1572 0.491473 0.240989841 MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [SWISSPROT;Acc:O94826]
0.118571 NKAP 812 0.453668 0.261360731
0.118612 RCC1 2455 0.5473 0.21672209 REGULATOR OF CHROMOSOME CONDENSATION (CELL CYCLE REGULATORY PROTEIN). [SWISSPROT;Acc:P18754]
0.118754 C1orf179 1065 0.47006 0.252635834 HYPORTHETICAL PROTEIN MGC27169. [RefSeq;Acc:NM_176782]
0.118945 CYP4A11 632 0.443397 0.268258468 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]
CYP4F2 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]
CYP4F8 631 CYTOCHROME P450 4F8 (EC 1.14.14.1) (CYPIVF8). [SWISSPROT;Acc:P98187]
0.11907 RSRC2 669 0.44632 0.266781681
0.11908 FLOT1 624 0.443899 0.268259221 FLOTILLIN-1. [SWISSPROT;Acc:O75955]
0.119287 ABHD14B 2705 0.574873 0.207501483
0.119541 DYNC1I2 375 0.428154 0.279200942 "DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC (DH IC-2) (CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2). [SWISSPROT;Acc:Q13409]"
0.119625 ARHGAP1 893 0.460314 0.259876954 RHO-GTPASE-ACTIVATING PROTEIN 1 (GTPASE-ACTIVATING PROTEIN RHOOGAP) (RHO-RELATED SMALL GTPASE PROTEIN ACTIVATOR) (CDC42 GTPASE-ACTIVATING PROTEIN) (P50-RHOGAP). [SWISSPROT;Acc:Q07960]
0.120354 TXNL4A 315 0.409455 0.293937063 SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN (DIM1 PROTEIN HOMOLOG) (THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD). [SWISSPROT;Acc:O14834]
0.120377 REV1 177 0.356839 0.337342611 REV1-LIKE; REV1 PROTEIN; REV1 (YEAST HOMOLOG)- LIKE. [RefSeq;Acc:NM_016316]
0.120499 STX1B 800 0.459899 0.262011877 SYNTAXIN 1B. [SWISSPROT;Acc:Q15531]
0.12066 SSR4 2838 0.62496 0.193068356 "TRANSLOCON-ASSOCIATED PROTEIN, DELTA SUBUNIT PRECURSOR (TRAP-DELTA) (SIGNAL SEQUENCE RECEPTOR DELTA SUBUNIT) (SSR-DELTA). [SWISSPROT;Acc:P51571]"
0.121 EHD1 2686 0.580932 0.208285996 EH-DOMAIN CONTAINING PROTEIN 1 (TESTILIN) (HPAST1). [SWISSPROT;Acc:Q9H4M9]
0.121116 YIF1A 939 0.472359 0.256406674 YIP1 INTERACTING FACTOR HOMOLOG; YIP1P-INTERACTING FACTOR; PUTATIVE RAB5-INTERACTING PROTEIN; PUTATIVE TRANSMEMBRANE PROTEIN 54TMP. [RefSeq;Acc:NM_020470]
0.121148 TUBG2 2126 0.531068 0.228121446 TUBULIN GAMMA-2 CHAIN (GAMMA-2 TUBULIN). [SWISSPROT;Acc:Q9NRH3]

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/