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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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 [...,...].
Hugo measured Gene final Rank description expected
Results: HTML CSV LaTeX Showing element 151 to 200 of 3206 in total
Hugo  : no value
measured
final
Rank
description
expected
0.0801834 0.219053395 2401 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.366045
0.0802494 0.24805925 1213 DYSTROPHIN. [SWISSPROT;Acc:P11532] 0.323509
0.0816437 0.064710307 3163 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 1.26168
0.081705 0.064710168 3166 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 1.26263
0.0828779 0.232079471 1913 HISTONE H4. [SWISSPROT;Acc:P02304] 0.35711
0.0840355 0.230505169 2021 "LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 0.364571
0.0856348 0.475139127 17 0.180231
0.0861167 0.236716356 1751 VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [SWISSPROT;Acc:O95670] 0.363797
0.086609 0.24374861 1431 ENTHOPROTIN; EPSIN 4; CLATHRIN INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION. [RefSeq;Acc:NM_014666] 0.355321
0.086859 0.223055688 2257 0.389405
0.0869771 0.268259065 626 0.324228
0.0884193 0.277370387 425 DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [RefSeq;Acc:NM_016355] 0.318777
0.0897053 0.209232998 2672 TRANSCRIPTION FACTOR MAFK (ERYTHROID TRANSCRIPTION FACTOR NF-E2 P18 SUBUNIT). [SWISSPROT;Acc:O60675] 0.428734
0.090945 0.26884454 614 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] 0.338281
0.0927584 0.253855101 1019 INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [SWISSPROT;Acc:Q15811] 0.365399
0.0942586 0.244862513 1367 HISTONE H2B.E (H2B/E). [SWISSPROT;Acc:Q99879] 0.384945
0.0943097 0.244862315 1371 HISTONE H2B. [RefSeq;Acc:NM_175055] 0.385154
0.0946163 0.244862399 1370 HISTONE H2B.S (H2B/S). [SWISSPROT;Acc:P57053] 0.386406
0.0948257 0.270031751 582 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 55 KDA REGULATORY SUBUNIT B, ALPHA ISOFORM (PP2A, SUBUNIT B, B-ALPHA ISOFORM) (PP2A, SUBUNIT B, B55-ALPHA ISOFORM) (PP2A, SUBUNIT B, PR55-ALPHA ISOFORM) (PP2A, SUBUNIT B, R2-ALPHA ISOFORM). [SWISSPROT;Acc:Q0" 0.351165
0.0957148 0.24486252 1365 HISTONE H2B.D (H2B/D). [SWISSPROT;Acc:Q99877] 0.390892
0.0979801 0.229073723 2079 LIM DOMAIN BINDING 1; CARBOXY TERMINAL LIM DOMAIN PROTEIN 2; LIM DOMAIN-BINDING FACTOR-1. [RefSeq;Acc:NM_003893] 0.427723
0.0979873 0.253442086 1024 UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [SWISSPROT;Acc:P55855] 0.386626
0.0999509 0.247160951 1260 ISCHEMIA/REPERFUSION INDUCIBLE PROTEIN. [RefSeq;Acc:NM_024640] 0.404396
0.100674 0.247383617 1251 "SIMILAR TO RIBOSOMAL PROTEIN, LARGE, P0. [SPTREMBL;Acc:Q96FQ9]" 0.406955
0.101691 0.197698946 2807 0.514373
0.101998 0.186791392 2878 RET FINGER PROTEIN 2 (LEUKEMIA ASSOCIATED PROTEIN 5) (B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA TUMOR SUPPRESSOR LEU5) (PUTATIVE TUMOR SUPPRESSOR RFP2) (TRIPARTITE MOTIF PROTEIN 13). [SWISSPROT;Acc:O60858] 0.546053
0.106596 0.219437634 2394 "BLOOM'S SYNDROME PROTEIN (EC 3.6.1.-) (RECQ PROTEIN-LIKE 3) (DNA HELICASE, RECQ-LIKE, TYPE 2). [SWISSPROT;Acc:P54132]" 0.485769
0.10808 0.205845886 2725 0.525053
0.109079 0.217096399 2446 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.502445
0.110079 0.248160981 1207 0.443579
0.112103 0.24268238 1504 GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEIN 12.3 (P205) (RECEPTOR OF ACTIVATED PROTEIN KINASE C 1) (RACK1) (RECEPTOR FOR ACTIVATED C KINASE). [SWISSPROT;Acc:P25388] 0.461933
0.112482 0.218734868 2409 0.514239
0.113218 0.267626375 654 CYSTEINE-RICH PROTEIN 1 (CYSTEINE-RICH INTESTINAL PROTEIN) (CRIP) (CYSTEINE-RICH HEART PROTEIN) (HCRHP). [SWISSPROT;Acc:P50238] 0.423045
0.11539 0.247389748 1250 BLOCK 23. [SPTREMBL;Acc:Q8NHW5] 0.46643
0.11603 0.255168577 985 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC. [RefSeq;Acc:NM_032569] 0.454719
0.116081 0.091904581 3109 "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]" 1.26306
0.116403 0.23021789 2032 0.505621
0.117829 0.261549868 810 0.450503
0.121841 0.268258207 633 F-ACTIN CAPPING PROTEIN ALPHA-2 SUBUNIT (CAPZ ALPHA-2). [SWISSPROT;Acc:P47755] 0.454193
0.122196 0.246463277 1275 PROTEASOME SUBUNIT BETA TYPE 9 PRECURSOR (EC 3.4.25.1) (PROTEASOME CHAIN 7) (MACROPAIN CHAIN 7) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX CHAIN 7) (RING12 PROTEIN) (LOW MOLECULAR MASS PROTEIN 2). [SWISSPROT;Acc:P28065] 0.495798
0.122792 0.231714934 1929 MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P38 (JTV-1 PROTEIN) (PRO0992). [SWISSPROT;Acc:Q13155] 0.529927
0.12467 0.24714192 1261 0.504447
0.126707 0.16882224 2920 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3 (EC 6.3.2.19) (UBIQUITIN- PROTEIN LIGASE) (UBIQUITIN CARRIER PROTEIN) (E2(17)KB 3). [SWISSPROT;Acc:P47986] 0.750535
0.127791 0.249563039 1161 ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA 1B SUBUNIT (SIGMA-ADAPTIN 1B) (ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1B SUBUNIT) (GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA-1B SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA- 1B SMALL CHAIN) (SIGMA 1B SUBUNIT OF AP-1 CL 0.512059
0.129279 0.222718189 2271 GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL 3-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:P32189] 0.58046
0.129655 0.246000861 1287 GUANINE NUCLEOTIDE-BINDING PROTEIN-LIKE 1 (GTP-BINDING PROTEIN HSR1). [SWISSPROT;Acc:P36915] 0.527051
0.130589 0.224864226 2220 60S RIBOSOMAL PROTEIN L21. [SWISSPROT;Acc:P46778] 0.580746
0.131767 0.222717838 2272 "GLYCEROL KINASE, TESTIS SPECIFIC 1 (EC 2.7.1.30) (ATP:GLYCEROL 3- PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). [SWISSPROT;Acc:Q14409]" 0.591632
0.135061 0.278606113 392 40S RIBOSOMAL PROTEIN S26. [SWISSPROT;Acc:P02383] 0.484774
0.135095 0.273980243 508 HEAT SHOCK FACTOR BINDING PROTEIN 1. [SWISSPROT;Acc:O75506] 0.493083

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/