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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Hugo final Gene description Rank expected measured
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Hugo  : no value
final
description
Rank
expected
measured
0.000219976 3206 0.7865 0.000173011
0.000219977 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 3204 0.81025 0.000178236
0.037315105 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]" 3187 0.772261 0.028817
0.062788394 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464] 3169 0.619812 0.038917
0.064710168 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]" 3166 1.26263 0.081705
0.064710307 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]" 3163 1.26168 0.0816437
0.065381634 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] 3149 0.996058 0.0651239
0.065381647 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357] 3148 0.988493 0.0646293
0.065381659 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355] 3147 0.99133 0.0648148
0.065381746 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] 3138 1.02411 0.0669581
0.068499095 "MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]" 3131 2.39209 0.163856
0.077606612 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333] 3123 0.874459 0.0678638
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]" 3109 1.26306 0.116081
0.097635809 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396] 3090 0.498014 0.048624
0.103197093 3069 0.517345 0.0533885
0.10668074 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8] 3049 0.293231 0.0312821
0.106743834 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262] 3042 0.366305 0.0391008
0.114763273 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT (BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT) (BTF2-P44) (GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2). [SWISSPROT;Acc:Q13888] 3034 1.27404 0.146213
0.119322081 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296] 3024 0.209553 0.0250043
0.126049126 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759] 3004 0.352603 0.0444453
0.128961526 GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60] 3001 0.392576 0.0506272
0.13955887 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 2983 0.222701 0.0310799
0.139559332 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 2978 0.221164 0.0308655
0.139559402 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 2976 0.223469 0.0311872
0.146163261 TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 2962 1.48707 0.217355
0.146165085 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 2960 0.510598 0.0746316
0.167885273 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551] 2923 2.16723 0.363846
0.168379781 PNAS-18. [SPTREMBL;Acc:Q9BZU3] 2921 1.80704 0.304269
0.16882224 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] 2920 0.750535 0.126707
0.174142655 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268] 2903 0.997527 0.173712
0.174700429 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735] 2902 0.999179 0.174557
0.178121277 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395] 2892 0.850269 0.151451
0.184481531 ADAPTER-RELATED PROTEIN COMPLEX 3 BETA 2 SUBUNIT (BETA-ADAPTIN 3B) (AP-3 COMPLEX BETA-3B SUBUNIT) (BETA-3B-ADAPTIN) (NEURON-SPECIFIC VESICLE COAT PROTEIN BETA-NAP). [SWISSPROT;Acc:Q13367] 2881 0.278146 0.0513128
0.186791392 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] 2878 0.546053 0.101998
0.188897649 2872 0.196598 0.0371369
0.188940513 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631] 2866 0.165297 0.0312313
0.188941031 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073] 2862 0.196899 0.0372023
0.188948413 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE ALPHA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 1) (1-AGPAT 1) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-ALPHA) (LPAAT-ALPHA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 1) (G15 PROTEIN). [SWISSPROT;Acc:Q9 2859 1.30479 0.246538
0.191276958 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072] 2852 4.39067 0.839834
0.193069178 "SUCCINATE DEHYDROGENASE [UBIQUINONE] CYTOCHROME B SMALL SUBUNIT, MITOCHONDRIAL PRECURSOR (CYBS) (SUCCINATE-UBIQUINONE REDUCTASE MEMBRANE ANCHOR SUBUNIT) (QPS2) (CII-4) (SUCCINATE DEHYDROGENASE COMPLEX SUBUNIT D) (SUCCINATE-UBIQUINONE OXIDOREDUCTASE CYTOCH" 2835 0.223379 0.0431276
0.193483258 ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 2827 0.833576 0.161283
0.197698946 2807 0.514373 0.101691
0.198811232 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]" 2799 0.287777 0.0572133
0.201399942 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0] 2773 0.100647 0.0202703
0.201617133 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6] 2769 0.241353 0.0486609
0.20161727 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2] 2768 0.282946 0.0570468
0.202098029 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771] 2767 1.60341 0.324046
0.205845886 2725 0.525053 0.10808
0.206548387 2723 0.1519 0.0313747
0.207336421 2716 1.98421 0.411399

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/