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 Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1276 histone h2b. [refseq;acc:nm_175055] Low confidence 203.671 199.194 1.02248
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] High confidence 171.231 167.177 1.02425
1277 histone h2b.s (h2b/s). [swissprot;acc:p57053] Low confidence 203.671 199.194 1.02248
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] High confidence 171.231 167.177 1.02425
1278 histone h2b.e (h2b/e). [swissprot;acc:q99879] Low confidence 203.671 199.194 1.02248
sestrin 3. [swissprot;acc:p58005] High confidence 218.368 213.219 1.02415
1279 protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Low confidence 200.75 196.336 1.02248
sestrin 2 (hi95). [swissprot;acc:p58004] High confidence 218.368 213.219 1.02415
1280 cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 213.22 1.02414
histone h2b.c (h2b/c). [swissprot;acc:q99880] Low confidence 203.672 199.196 1.02247
1281 cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] High confidence 218.368 213.22 1.02414
histone h2b.d (h2b/d). [swissprot;acc:q99877] Low confidence 203.671 199.195 1.02247
1282 connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [swissprot;acc:p29279] 208.383 203.805 1.02246
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] High confidence 218.368 213.22 1.02414
1283 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Low confidence 205.134 200.628 1.02246
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] High confidence 218.368 213.22 1.02414
1284 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
fumarylacetoacetase (ec 3.7.1.2) (fumarylacetoacetate hydrolase) (beta-diketonase) (faa). [swissprot;acc:p16930] Low confidence 202.294 197.852 1.02245
1285 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] High confidence 218.368 213.22 1.02414
prohibitin. [swissprot;acc:p35232] Low confidence 186.195 182.109 1.02244
1286 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 218.368 213.22 1.02414
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Low confidence 202.806 198.355 1.02244
1287 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] High confidence 218.368 213.22 1.02414
long-chain-fatty-acid--coa ligase 3 (ec 6.2.1.3) (long-chain acyl-coa synthetase 3) (lacs 3). [swissprot;acc:o95573] Low confidence 201.127 196.714 1.02243
1288 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] High confidence 218.368 213.22 1.02414
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Low confidence 204.236 199.757 1.02242
1289 flotillin-1. [swissprot;acc:o75955] High confidence 218.368 213.22 1.02414
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Low confidence 203.073 198.619 1.02242
1290 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] 195.789 191.498 1.02241
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

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/