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 2875 to 2924 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1438 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Subtracted 3886.62 3438.82 447.8
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Divided 6721.25 7238.34 1.07693
1439 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 5658.8 6093.56 1.07683
limkain beta 2. [refseq;acc:nm_025140] Subtracted 5796.03 6243.78 447.75
1440 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 6296.52 6743.85 447.33
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Divided 6522.96 7023.77 1.07678
1441 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Subtracted 5728.92 6175.99 447.07
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Divided 6216.12 6693.38 1.07678
1442 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Subtracted 6213.27 6659.39 446.12
proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] Divided 6216.13 6693.13 1.07674
1443 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Subtracted 5657.71 6103.57 445.86
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Divided 5450.9 5869.07 1.07672
1444 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Subtracted 5657.71 6103.54 445.83
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Divided 5450.9 5869.07 1.07672
1445 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 5117.85 5510.45 1.07671
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Subtracted 5657.71 6103.54 445.83
1446 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Divided 5117.85 5510.45 1.07671
1447 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Subtracted 5657.72 6103.52 445.8
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Divided 5117.85 5510.45 1.07671
1448 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Subtracted 5657.72 6103.52 445.8
dpy-30-like protein. [swissprot;acc:q9c005] Divided 5602.01 6031.05 1.07659
1449 methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Subtracted 6436.73 6882.16 445.43
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Divided 5602.01 6031.05 1.07659
1450 calmegin precursor. [swissprot;acc:o14967] Subtracted 5910.06 6355.08 445.02
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Divided 5602.01 6031.05 1.07659
1451 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Subtracted 5910.06 6355.08 445.02
neighbor of cox4. [swissprot;acc:o43402] Divided 5602.01 6031.05 1.07659
1452 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Subtracted 5910.06 6355.08 445.02
1453 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 5602.01 6031.05 1.07659
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Subtracted 5910.06 6355.08 445.02
1454 ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Divided 5770.74 6210.65 1.07623
wd-repeat protein 3. [swissprot;acc:q9unx4] Subtracted 4039.81 4484.22 444.41
1455 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] 5945.56 6389.63 444.07
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Divided 5672.68 6104.68 1.07615
1456 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 5672.25 6104.01 1.07612
myosin viia. [swissprot;acc:q13402] Subtracted 5759.68 6203.63 443.95
1457 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 5672.23 6103.98 1.07612
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] Subtracted 5759.68 6203.63 443.95
1458 mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Divided 5672.25 6104.01 1.07612
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] Subtracted 5759.68 6203.63 443.95
1459 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Divided 5672.25 6104.01 1.07612
eif-5a2 protein. [refseq;acc:nm_020390] Subtracted 6222.4 6665.83 443.43
1460 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 5996.14 6439.46 443.32
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Divided 5696.65 6130.26 1.07612
1461 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] Subtracted 5457.14 5899.85 442.71
9 kda protein. [swissprot;acc:p13994] Divided 5672.25 6104.01 1.07612
1462 eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Subtracted 6212.98 6655.12 442.14
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Divided 5672.24 6103.99 1.07612

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/