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 expected measured Rank Gene description
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
Hugo  : no value
final
expected
measured
Rank
description
0.000219976 0.7865 0.000173011 3206
0.000219977 0.81025 0.000178236 3204 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915]
0.037315105 0.772261 0.028817 3187 "PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 14C; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-81; PKC-POTENTIATED PP1 INHIBITORY PROTEIN. [RefSeq;Acc:NM_030949]"
0.062788394 0.619812 0.038917 3169 RIBOSOMAL PROTEIN S6 KINASE-LIKE 1. [RefSeq;Acc:NM_031464]
0.064710168 1.26263 0.081705 3166 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE ALPHA ISOFORM (MYHC-ALPHA). [SWISSPROT;Acc:P13533]"
0.064710307 1.26168 0.0816437 3163 "MYOSIN HEAVY CHAIN, CARDIAC MUSCLE BETA ISOFORM (MYHC-BETA). [SWISSPROT;Acc:P12883]"
0.065381634 0.996058 0.0651239 3149 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358]
0.065381647 0.988493 0.0646293 3148 MELANOMA-ASSOCIATED ANTIGEN 3 (MAGE-3 ANTIGEN) (ANTIGEN MZ2-D). [SWISSPROT;Acc:P43357]
0.065381659 0.99133 0.0648148 3147 MELANOMA-ASSOCIATED ANTIGEN 1 (MAGE-1 ANTIGEN) (ANTIGEN MZ2-E). [SWISSPROT;Acc:P43355]
0.065381746 1.02411 0.0669581 3138 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932]
0.068499095 2.39209 0.163856 3131 "MYOSIN VA (MYOSIN 5A) (DILUTE MYOSIN HEAVY CHAIN, NON-MUSCLE) (MYOSIN HEAVY CHAIN 12) (MYOXIN). [SWISSPROT;Acc:Q9Y4I1]"
0.077606612 0.874459 0.0678638 3123 NUCLEAR DNA-BINDING PROTEIN; SMALL UNIQUE NUCLEAR RECEPTOR COREPRESSOR; C1D DNA-BINDING PROTEIN. [RefSeq;Acc:NM_006333]
0.091904581 1.26306 0.116081 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]"
0.097635809 0.498014 0.048624 3090 METHYLTRANSFERASE LIKE 2. [RefSeq;Acc:NM_018396]
0.103197093 0.517345 0.0533885 3069
0.10668074 0.293231 0.0312821 3049 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-5 LIKE SUBUNIT. [SWISSPROT;Acc:Q9Y3K8]
0.106743834 0.366305 0.0391008 3042 GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) GAMMA-7 SUBUNIT. [SWISSPROT;Acc:O60262]
0.114763273 1.27404 0.146213 3034 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]
0.119322081 0.209553 0.0250043 3024 SYNBINDIN (TRS23 HOMOLOG) (HEMATOPOIETIC STEM/PROGENITOR CELL PROTEIN 172) (HSPC172) (PTD009) (CGI-104). [SWISSPROT;Acc:Q9Y296]
0.126049126 0.352603 0.0444453 3004 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [RefSeq;Acc:NM_022759]
0.128961526 0.392576 0.0506272 3001 GABA-A RECEPTOR-ASSOCIATED PROTEIN. [SPTREMBL;Acc:Q9BY60]
0.13955887 0.222701 0.0310799 2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056]
0.139559332 0.221164 0.0308655 2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630]
0.139559402 0.223469 0.0311872 2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017]
0.146163261 1.48707 0.217355 2962 TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111]
0.146165085 0.510598 0.0746316 2960 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211]
0.167885273 2.16723 0.363846 2923 CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551]
0.168379781 1.80704 0.304269 2921 PNAS-18. [SPTREMBL;Acc:Q9BZU3]
0.16882224 0.750535 0.126707 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]
0.174142655 0.997527 0.173712 2903 60S RIBOSOMAL PROTEIN L22 (EPSTEIN-BARR VIRUS SMALL RNA ASSOCIATED PROTEIN) (EBER ASSOCIATED PROTEIN) (EAP) (HEPARIN BINDING PROTEIN HBP15). [SWISSPROT;Acc:P35268]
0.174700429 0.999179 0.174557 2902 TYROSINE AMINOTRANSFERASE (EC 2.6.1.5) (L-TYROSINE:2-OXOGLUTARATE AMINOTRANSFERASE) (TAT). [SWISSPROT;Acc:P17735]
0.178121277 0.850269 0.151451 2892 UBIQUITIN ACTIVATING ENZYME E1-LIKE PROTEIN. [RefSeq;Acc:NM_006395]
0.184481531 0.278146 0.0513128 2881 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]
0.186791392 0.546053 0.101998 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]
0.188897649 0.196598 0.0371369 2872
0.188940513 0.165297 0.0312313 2866 HEPATOMA-DERIVED GROWTH FACTOR-RELATED PROTEIN 2. [RefSeq;Acc:NM_032631]
0.188941031 0.196899 0.0372023 2862 CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073]
0.188948413 1.30479 0.246538 2859 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
0.191276958 4.39067 0.839834 2852 SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEATS 2. [RefSeq;Acc:NM_019072]
0.193069178 0.223379 0.0431276 2835 "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"
0.193483258 0.833576 0.161283 2827 ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7]
0.197698946 0.514373 0.101691 2807
0.198811232 0.287777 0.0572133 2799 "ATAXIN 2; OLIVOPONTOCEREBELLAR ATAXIA 2, AUTOSOMAL DOMINANT. [RefSeq;Acc:NM_002973]"
0.201399942 0.100647 0.0202703 2773 DJ570F3.6 (NOVEL PROTEIN SIMILAR TO LYSOPHOSPHOLIPASE II (LYPLA2)). [SPTREMBL;Acc:Q9UGE0]
0.201617133 0.241353 0.0486609 2769 SIMILAR TO ZINC FINGER PROTEIN 277. [SPTREMBL;Acc:Q8WWA6]
0.20161727 0.282946 0.0570468 2768 ZINC FINGER PROTEIN 277. [SWISSPROT;Acc:Q9NRM2]
0.202098029 1.60341 0.324046 2767 HELICASE (FRAGMENT). [SPTREMBL;Acc:Q92771]
0.205845886 0.525053 0.10808 2725
0.206548387 0.1519 0.0313747 2723
0.207336421 1.98421 0.411399 2716

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/