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 Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7462 to 7511 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Interaction Map
Network Comparison Type
red
green
network_comparison
1866 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Low confidence Subtracted 201.162 197.241 3.921
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] High confidence Divided 221.725 224.133 1.01086
wd repeat endosomal protein. [refseq;acc:nm_020839] Low confidence 201.234 197.313 1.01987
1867 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 199.922 196.027
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] High confidence 203.071 200.89 1.01086
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Subtracted 210.856 213.147 2.291
wd repeat endosomal protein. [refseq;acc:nm_020839] Low confidence 201.234 197.313 3.921
1868 60s ribosomal protein l28. [swissprot;acc:p46779] High confidence 215.896 213.61 2.286
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Low confidence Divided 199.127 195.25 1.01986
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Subtracted 201.157 197.236 3.921
protein kinase nyd-sp25. [refseq;acc:nm_033516] High confidence Divided 207.642 209.895 1.01085
1869 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Subtracted 218.414 216.131 2.283
lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] Divided 220.107 217.75 1.01082
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Low confidence Subtracted 200.267 196.347 3.92
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Divided 203.016 199.062 1.01986
1870 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] High confidence 220.107 217.75 1.01082
nag14 protein. [refseq;acc:nm_022143] Low confidence Subtracted 200.267 196.347 3.92
neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359] Divided 199.289 195.409 1.01986
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] High confidence Subtracted 212.186 214.467 2.281
1871 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Divided 222.819 225.228 1.01081
dj467n11.1 protein. [refseq;acc:nm_022091] Low confidence Subtracted 199.184 195.266 3.918
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] High confidence 212.186 214.467 2.281
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Low confidence Divided 201.627 197.703 1.01985
1872 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Subtracted 200.092 196.175 3.917
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] High confidence Divided 222.819 225.228 1.01081
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] Subtracted 212.186 214.467 2.281
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Low confidence Divided 202.408 198.469 1.01985
1873 10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 203.414 199.455
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Subtracted 200.522 196.605 3.917
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] High confidence 193.1 190.823 2.277
scratch; scratch 1. [refseq;acc:nm_031309] Divided 210.55 208.305 1.01078
1874 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] Low confidence 200.85 196.94 1.01985
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Subtracted 205.081 201.165 3.916
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] High confidence 193.138 190.861 2.277
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Divided 223.862 226.271 1.01076
1875 dek protein. [swissprot;acc:p35659] Low confidence 203.415 199.456 1.01985
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] High confidence Subtracted 193.111 190.834 2.277
pyridoxal kinase (ec 2.7.1.35) (pyridoxine kinase). [swissprot;acc:o00764] Low confidence 199.417 195.501 3.916
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] High confidence Divided 223.862 226.271 1.01076
1876 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Low confidence Subtracted 205.081 201.165 3.916
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] High confidence 185.276 187.534 2.258
myosin vi. [swissprot;acc:q9um54] Low confidence Divided 203.415 199.456 1.01985
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] High confidence 223.862 226.271 1.01076
1877 branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Low confidence 199.88 195.99 1.01985
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] High confidence 212.186 214.467 1.01075
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Low confidence Subtracted 198.893 194.978 3.915
protein kinase nyd-sp25. [refseq;acc:nm_033516] High confidence 207.642 209.895 2.253
1878 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Divided 212.186 214.467 1.01075
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Low confidence Subtracted 198.893 194.978 3.915
scratch; scratch 1. [refseq;acc:nm_031309] High confidence 210.55 208.305 2.245

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
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/