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 Interaction Map description Value Type Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Interaction Map
description
green
red
network_comparison
251 High confidence oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 166.661 186.172 1.11707
Low confidence nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 201.035 210.415 1.04666
252 High confidence eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 237.292 1.11689
Low confidence cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] 201.035 210.414 1.04665
253 High confidence mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 228 1.11583
Low confidence nadph oxidase 4. [refseq;acc:nm_016931] 201.035 210.413 1.04665
254 High confidence source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 179.88 200.691 1.11569
Low confidence nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 201.035 210.414 1.04665
255 High confidence oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 179.88 200.691 1.11569
Low confidence nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 201.035 210.413 1.04665
256 High confidence max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 227.999 1.11569
Low confidence oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 190.521 199.376 1.04648
257 High confidence dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 179.88 200.691 1.11569
Low confidence tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 192.404 201.316 1.04632
258 High confidence max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 227.999 1.11564
Low confidence tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 192.427 201.304 1.04613
259 High confidence max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 227.999 1.11562
Low confidence trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 202.482 211.794 1.04599
260 High confidence c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 1.11394
Low confidence ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 207.34 216.855 1.04589
261 High confidence heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 196.978 219.421 1.11394
Low confidence ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 207.333 216.845 1.04588
262 High confidence heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 196.978 219.421 1.11394
Low confidence breast cancer antigen ny-br-1. [refseq;acc:nm_052997] 207.332 216.842 1.04587
263 High confidence heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 196.978 219.421 1.11394
Low confidence sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] 207.063 216.546 1.0458
264 High confidence mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 196.978 219.421 1.11394
Low confidence senescence downregulated leo1-like. [refseq;acc:nm_138792] 207.063 216.546 1.0458
265 High confidence splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 202.459 225.217 1.11241
Low confidence solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] 207.063 216.546 1.0458
266 High confidence transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 267.88 241.07 1.11121
Low confidence calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] 205.509 214.887 1.04563
267 High confidence density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 267.88 241.07 1.11121
Low confidence tensin. [refseq;acc:nm_022648] 205.872 215.258 1.04559
268 High confidence eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 244.167 271.016 1.10996
Low confidence sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] 199.455 208.469 1.04519
269 High confidence cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 267.352 241.373 1.10763
Low confidence sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] 199.44 208.436 1.04511
270 High confidence fad synthetase. [refseq;acc:nm_025207] 267.352 241.373 1.10763
Low confidence ring finger protein 10. [refseq;acc:nm_014868] 199.44 208.437 1.04511
271 High confidence bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 267.352 241.373 1.10763
Low confidence tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] 192.595 201.219 1.04478
272 High confidence ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 267.352 241.373 1.10763
Low confidence odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 208.421 217.69 1.04447
273 High confidence bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] 267.352 241.373 1.10763
Low confidence parafibromin. [refseq;acc:nm_024529] 204.916 214.015 1.0444
274 High confidence nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 267.352 241.373 1.10763
Low confidence kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 200.653 209.532 1.04425
275 High confidence cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 267.352 241.373 1.10763
Low confidence dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 191.203 199.66 1.04423

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/