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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measured Rank Gene expected description Hugo final
Results: HTML CSV LaTeX Showing element 2908 to 2957 of 3206 in total
measured
Rank
expected
description
Hugo
final
0.517862 1315 2.1077 HYDROXYACID OXIDASE 1 (EC 1.1.3.15) (HAOX1) (GLYCOLATE OXIDASE) (GOX). [SWISSPROT;Acc:Q9UJM8] HAO1 0.245700052
0.517899 2073 2.25773 N-ACETYLGLUTAMATE SYNTHASE. [RefSeq;Acc:NM_153006] NAGS 0.229389254
0.517911 1317 2.10824 ATP-DEPENDENT RNA HELICASE MGC2835; ATP-DEPENDENT RNA HELICASE; APOPTOSIS RELATED PROTEIN APR-5; DEAD BOX HELICASE 97 KDA. [RefSeq;Acc:NM_024072] DDX54 0.245660361
0.518099 1749 2.18869 VACUOLAR ATP SYNTHASE SUBUNIT D (EC 3.6.3.14) (V-ATPASE D SUBUNIT) (VACUOLAR PROTON PUMP D SUBUNIT) (V-ATPASE 28 KDA ACCESSORY PROTEIN). [SWISSPROT;Acc:Q9Y5K8] ATP6V1D 0.236716483
0.518329 2977 3.71404 RETINAL SHORT-CHAIN DEHYDROGENASE/REDUCTASE 3. [RefSeq;Acc:NM_016246] HSD17B14 0.139559348
0.518333 2393 2.36093 SERINE/THREONINE PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT (EC 3.1.3.16) (PP-1G). [SWISSPROT;Acc:P36873] PPP1CC 0.219546111
0.522708 2478 2.41413 GALECTIN-9 (HOM-HD-21) (ECALECTIN). [SWISSPROT;Acc:O00182] LGALS9 0.216520237
0.525129 1990 2.27455 DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (EC 2.7.7.6) (RPB1). [SWISSPROT;Acc:P24928] POLR2A 0.230871601
0.526405 2588 2.47257 HAGHL 0.212897916
0.52666 712 1.98825 HISTONE DEACETYLASE 2 (HD2). [SWISSPROT;Acc:Q92769] no value 0.264886206
0.527178 887 2.02856 KINESIN LIGHT CHAIN 2 (KLC 2). [SWISSPROT;Acc:Q9H0B6] KLC2 0.259877943
0.527851 1987 2.28589 60S RIBOSOMAL PROTEIN L12. [SWISSPROT;Acc:P30050] no value 0.230917061
0.528875 723 1.99819 ACTIN-LIKE PROTEIN 3 (ACTIN-RELATED PROTEIN 3) (ACTIN-2). [SWISSPROT;Acc:P32391] ACTR3 0.264677033
0.529846 1400 2.17049 PROTEASOME SUBUNIT ALPHA TYPE 4 (EC 3.4.25.1) (PROTEASOME COMPONENT C9) (MACROPAIN SUBUNIT C9) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C9) (PROTEASOME SUBUNIT L). [SWISSPROT;Acc:P25789] PSMA4 0.244113541
0.532733 2051 2.31678 "COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING PROTEIN 1) (P32) (P33). [SWISSPROT;Acc:Q07021]" C1QBP 0.229945442
0.533046 2798 2.66667 WD REPEAT- AND FYVE DOMAIN-CONTAINING PROTEIN 2; WD40 AND FYVE DOMAIN CONTAINING 2. [RefSeq;Acc:NM_052950] WDFY2 0.199892
0.533964 2009 2.31472 NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [SWISSPROT;Acc:P22392] no value 0.230681897
0.534301 515 1.96129 ATAXIN 2-BINDING PROTEIN. [SWISSPROT;Acc:Q9NWB1] 0.272423252
0.535221 221 1.68161 B9D2 0.318278911
0.53545 1828 2.28647 S-ADENOSYLMETHIONINE SYNTHETASE ALPHA AND BETA FORMS (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-I/III). [SWISSPROT;Acc:Q00266] MAT1A 0.234181949
0.536283 1500 2.20914 WDR75 0.242756457
0.537765 594 1.99671 PHOSPHOACETYLGLUCOSAMINE MUTASE (EC 5.4.2.3) (PAGM) (ACETYLGLUCOSAMINE PHOSPHOMUTASE) (N-ACETYLGLUCOSAMINE-PHOSPHATE MUTASE) (PHOSPHOGLUCOMUTASE 3). [SWISSPROT;Acc:O95394] PGM3 0.269325541
0.539175 560 1.99055 ELAV-LIKE PROTEIN 3 (HU-ANTIGEN C) (HUC) (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIATED ANTIGEN) (PARANEOPLASTIC LIMBIC ENCEPHALITIS ANTIGEN 21). [SWISSPROT;Acc:Q14576] no value 0.270867348
0.539817 2443 2.48653 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.217096516
0.539944 1441 2.21735 UTP15 0.243508693
0.539996 279 1.77667 CYTOPLASMIC PROTEIN NCK1 (NCK ADAPTOR PROTEIN 1) (SH2/SH3 ADAPTOR PROTEIN NCK-ALPHA). [SWISSPROT;Acc:P16333] NCK1 0.303937141
0.541146 1979 2.34239 60S RIBOSOMAL PROTEIN L10A (CSA-19). [SWISSPROT;Acc:P53025] no value 0.231023015
0.541777 513 1.98406 NUCLEAR PROTEIN SKIP (SKI-INTERACTING PROTEIN) (SNW1 PROTEIN) (NUCLEAR RECEPTOR COACTIVATOR NCOA-62). [SWISSPROT;Acc:Q13573] SNW1 0.273064827
0.542979 2707 2.61855 no value 0.207358653
0.543161 1997 2.35379 40S RIBOSOMAL PROTEIN S14 (PRO2640). [SWISSPROT;Acc:P06366] RPS14 0.230760178
1998 40S RIBOSOMAL PROTEIN S18 (KE-3) (KE3). [SWISSPROT;Acc:P25232] no value
0.544593 678 2.04792 TUBULIN TYROSINE LIGASE-LIKE PROTEIN HOTTL (HQP0207). [SWISSPROT;Acc:Q9Y4R7] BRPF1 0.265924938
0.54526 1483 2.24437 NOL14 0.242945682
0.546429 929 2.12125 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG (SUI1ISO1). [SWISSPROT;Acc:P41567] EIF1 0.257597643
0.547661 240 1.75288 "5'-AMP-ACTIVATED PROTEIN KINASE, CATALYTIC ALPHA-1 CHAIN (EC 2.7.1.-) (AMPK ALPHA-1 CHAIN). [SWISSPROT;Acc:Q13131]" PRKAA1 0.312434964
0.549251 2480 2.53881 CHROMODOMAIN Y-LIKE PROTEIN 2. [RefSeq;Acc:NM_152342] CDYL2 0.216341908
0.549308 1902 2.36366 no value 0.232397214
0.552551 758 2.09375 43 KDA RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE (RAPSYN) (ACETYLCHOLINE RECEPTOR-ASSOCIATED 43 KDA PROTEIN) (43 KDA POSTSYNAPTIC PROTEIN). [SWISSPROT;Acc:Q13702] RAPSN 0.263904955
0.553061 966 2.16185 PROTEIN TRANSLATION FACTOR SUI1 HOMOLOG GC20. [SWISSPROT;Acc:O60739] EIF1B 0.255827648
0.553489 2708 2.66927 VERY-LONG-CHAIN ACYL-COA SYNTHETASE (EC 6.2.1.-) (VERY-LONG-CHAIN- FATTY-ACID-COA LIGASE). [SWISSPROT;Acc:O14975] SLC27A2 0.207355944
0.553815 628 2.06448 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] SESN2 0.268258835
0.555029 337 1.94761 M-PHASE INDUCER PHOSPHATASE 1 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25A). [SWISSPROT;Acc:P30304] CDC25A 0.284979539
0.556589 1880 2.39113 VACUOLAR ATP SYNTHASE 16 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14). [SWISSPROT;Acc:P27449] ATP6V0C 0.232772371
0.557721 275 1.82999 SPLICING FACTOR 3B SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 145) (SAP 145) (SF3B150) (PRE-MRNA SPLICING FACTOR SF3B 145 KDA SUBUNIT). [SWISSPROT;Acc:Q13435] SF3B2 0.304767239
0.557991 125 1.56247 C9orf41 0.357121097
0.558539 2661 2.66089 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 (EC 2.7.7.41) (CDP-DIGLYCERIDE SYNTHETASE 1) (CDP-DIGLYCERIDE PYROPHOSPHORYLASE 1) (CDP- DIACYLGLYCEROL SYNTHASE 1) (CDS 1) (CTP:PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1) (CDP-DAG SYNTHASE 1) (CDP-DG SYNTHETASE 1). [Source CDS1 0.209906836
0.562114 1506 2.31688 WD-REPEAT PROTEIN BING4. [SWISSPROT;Acc:O15213] WDR46 0.242616795
0.56263 1497 2.31748 T-CELL ACTIVATION WD REPEAT PROTEIN. [RefSeq;Acc:NM_139281] WDR36 0.242776637
0.562681 2192 2.48806 MEVALONATE KINASE (EC 2.7.1.36) (MK). [SWISSPROT;Acc:Q03426] MVK 0.226152504
0.563143 499 2.05361 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] no value 0.274221006

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/