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 5158 to 5207 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1290 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Ranked 218.368 213.22 1.02414
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] Rooted 53.457 55.8006 1.04384
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Squared 24597.8 27791.6 1.12984
1291 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Measured 5655.85 6120.64 1.08218
grb2-related adaptor protein. [swissprot;acc:q13588] Squared 29854.9 33731 1.12983
hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Ranked 221.093 226.399 1.024
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Rooted 65.8578 68.7414 1.04379
1292 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Ranked 233.942 228.46 1.024
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Measured 5655.85 6120.64 1.08218
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Rooted 56.8891 54.5075 1.04369
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Squared 28010 31646.5 1.12983
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] Ranked 233.942 228.46 1.024
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Rooted 56.8889 54.5073 1.04369
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Measured 5655.85 6120.64 1.08218
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Squared 28010 31646.5 1.12983
1294 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Ranked 221.093 226.399 1.024
lbp-9. [refseq;acc:nm_014553] Squared 28010 31646.5 1.12983
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Rooted 60.5034 63.1459 1.04368
sestrin 3. [swissprot;acc:p58005] Measured 5655.85 6120.65 1.08218
1295 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 6120.64
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Ranked 221.093 226.399 1.024
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Squared 28010 31646.5 1.12983
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Rooted 53.2742 51.0444 1.04368
1296 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 61.662 64.3527 1.04364
flotillin-1. [swissprot;acc:o75955] Measured 5655.85 6120.64 1.08218
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Ranked 209.062 204.174 1.02394
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Squared 14199.7 16043 1.12981
1297 proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Ranked 209.062 204.174 1.02394
proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] Rooted 62.5036 65.2268 1.04357
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Squared 37489.2 33182.9 1.12977
sestrin 2 (hi95). [swissprot;acc:p58004] Measured 5655.85 6120.65 1.08218
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] Ranked 206.482 211.404 1.02384
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Rooted 56.8983 54.5263 1.0435
sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] Measured 5655.85 6120.62 1.08218
t54 protein. [swissprot;acc:q92917] Squared 37489.2 33182.9 1.12977
1299 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Measured 5589.33 6047.9 1.08204
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Ranked 217.635 212.575 1.0238
mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] Rooted 60.5069 63.1346 1.04343
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Squared 27297.6 30839.2 1.12974
1300 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Measured 5589.33 6047.9 1.08204
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Ranked 217.634 212.576 1.02379
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Squared 14419.4 16287.9 1.12958
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Rooted 60.5069 63.1346 1.04343
1301 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Measured 6618.74 7161.67 1.08203
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Rooted 61.5001 64.1696 1.04341
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Squared 14245.7 16091.1 1.12954
tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] Ranked 206.852 211.757 1.02371
1302 peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Measured 6343.26 6862.94 1.08193
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Rooted 65.6777 68.5272 1.04339
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Ranked 217.624 212.584 1.02371

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/