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 Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2580 to 2629 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1290 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] High confidence 218.368 213.22 1.02414
1291 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 221.093 226.399 1.024
long-chain-fatty-acid--coa ligase 4 (ec 6.2.1.3) (long-chain acyl-coa synthetase 4) (lacs 4). [swissprot;acc:o60488] Low confidence 201.117 196.709 1.02241
1292 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 200.544 196.152 1.02239
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] High confidence 233.942 228.46 1.024
1293 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]
paraspeckle protein 1. [refseq;acc:nm_018282] Low confidence 200.543 196.152 1.02239
1294 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] High confidence 221.093 226.399 1.024
yeast sec31p homolog. [refseq;acc:nm_014933] Low confidence 204.144 199.676 1.02238
1295 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] High confidence 221.093 226.399 1.024
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Low confidence 199.695 195.323 1.02238
1296 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] High confidence 209.062 204.174 1.02394
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Low confidence 204.174 199.705 1.02238
1297 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] 200.193 195.812 1.02237
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] High confidence 209.062 204.174 1.02394
1298 dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [swissprot;acc:p10515] 206.482 211.404 1.02384
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Low confidence 203.074 198.63 1.02237
1299 aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:q99798] 200.342 195.959
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] High confidence 217.635 212.575 1.0238
1300 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 217.634 212.576 1.02379
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Low confidence 199.276 194.918 1.02236
1301 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] High confidence 206.852 211.757 1.02371
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Low confidence 199.276 194.918 1.02236
1302 proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] High confidence 217.624 212.584 1.02371
1303 activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 269.157 275.531 1.02368
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Low confidence 199.276 194.918 1.02236
1304 glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] High confidence 207.387 212.275 1.02357
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Low confidence 199.275 194.918 1.02235
1305 glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [swissprot;acc:q9hcl2] 204.064 199.602
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] High confidence 218.439 213.436 1.02344
1306 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Low confidence 199.275 194.918 1.02235
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] High confidence 218.441 213.441 1.02343
1307 myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613] Low confidence 204.064 199.602 1.02235
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] High confidence 218.44 213.44 1.02343
1308 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Low confidence 199.268 194.914 1.02234
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] High confidence 218.44 213.439 1.02343
1309 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 226.439 221.26 1.02341
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Low confidence 200.536 196.157 1.02232
1310 p66 alpha. [refseq;acc:nm_017660] 229.478 224.473 1.0223
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] High confidence 226.439 221.26 1.02341
1311 transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Low confidence 229.478 224.473 1.0223
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] High confidence 226.439 221.26 1.02341
1312 rad50 homolog isoform 1. [refseq;acc:nm_005732] 199.739 204.407 1.02337
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Low confidence 229.478 224.473 1.0223
1313 serologically defined colon cancer antigen 1. [refseq;acc:nm_004713] 202.396 197.985 1.02228
signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763] High confidence 222.573 227.75 1.02326
1314 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Low confidence 201.948 197.549 1.02227
signal transducer and activator of transcription 4. [swissprot;acc:q14765] High confidence 222.573 227.751 1.02326
1315 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Low confidence 206.697 202.196 1.02226

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/