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 2900 to 2949 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1450 microtubule-associated protein 7. [refseq;acc:nm_003980] Low confidence 7686.1 7949.9 1.03432
1451 n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 8174.49 8454.8 1.03429
neighbor of cox4. [swissprot;acc:o43402] High confidence 5602.01 6031.05 1.07659
1452 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6]
sorbitol dehydrogenase (ec 1.1.1.14) (l-iditol 2-dehydrogenase). [swissprot;acc:q00796] Low confidence 8116.02 8394.32 1.03429
1453 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] High confidence 5602.01 6031.05 1.07659
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Low confidence 7795.39 8062.73 1.03429
1454 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] 8155.72 8435.4
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] High confidence 5770.74 6210.65 1.07623
1455 high-affinity cationic amino acid transporter-1 (cat-1) (cat1) (system y+ basic amino acid transporter) (ecotropic retroviral leukemia receptor homolog) (err) (ecotropic retrovirus receptor homolog). [swissprot;acc:p30825] Low confidence 8112.74 8390.82 1.03428
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] High confidence 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
rna binding protein. [refseq;acc:nm_032509] Low confidence 7796.51 8063.81 1.03428
1457 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] High confidence 5672.23 6103.98 1.07612
synaptosomal-associated protein 25 (snap-25) (super protein) (sup). [swissprot;acc:p13795] Low confidence 8215.37 8496.97 1.03428
1458 leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243] 7796.51 8063.81
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] High confidence 5672.25 6104.01 1.07612
1459 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Low confidence 7796.51 8063.81 1.03428
1460 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] High confidence 5696.65 6130.26 1.07612
synaptosomal-associated protein 23 (snap-23) (vesicle-membrane fusion protein snap-23). [swissprot;acc:o00161] Low confidence 8215.37 8496.97 1.03428
1461 9 kda protein. [swissprot;acc:p13994] High confidence 5672.25 6104.01 1.07612
solute carrier family 2, facilitated glucose transporter, member 5 (glucose transporter type 5, small intestine) (fructose transporter). [swissprot;acc:p22732] Low confidence 7863.59 8133.06 1.03427
1462 solute carrier family 2, facilitated glucose transporter, member 11 (glucose transporter type 11) (glucose transporter type 10). [swissprot;acc:q9byw1] 7863.42 8132.93
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] High confidence 5672.24 6103.99 1.07612
1463 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 5672.2 6103.92 1.07611
solute carrier family 2, facilitated glucose transporter, member 9 (glucose transporter type 9). [swissprot;acc:q9nrm0] Low confidence 7863.53 8133.01 1.03427
1464 solute carrier family 2, facilitated glucose transporter, member 2 (glucose transporter type 2, liver). [swissprot;acc:p11168] 7863.9 8133.29 1.03426
zasp protein (fragment). [sptrembl;acc:q9y4z3] High confidence 5671.93 6103.49 1.07609
1465 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 5686.74 6119.36 1.07608
solute carrier family 2, facilitated glucose transporter, member 4 (glucose transporter type 4, insulin-responsive). [swissprot;acc:p14672] Low confidence 7864.08 8133.43 1.03425
1466 glucose transporter 14. [refseq;acc:nm_153449] 7864.04 8133.4
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] High confidence 6523.17 7019.44 1.07608
1467 p47 protein isoform a. [refseq;acc:nm_016143] 6444.4 6932.39 1.07572
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Low confidence 7643.48 7905.28 1.03425
1468 solute carrier family 2, facilitated glucose transporter, member 3 (glucose transporter type 3, brain). [swissprot;acc:p11169] 7864.07 8133.43
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] High confidence 5473.09 5887.45 1.07571
1469 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
low-affinity cationic amino acid transporter-2 (cat-2) (cat2). [swissprot;acc:p52569] Low confidence 8113.16 8391 1.03425
1470 85 kda calcium-independent phospholipase a2 (ec 3.1.1.4) (ipla2) (cai- pla2) (group vi phospholipase a2) (gvi pla2). [swissprot;acc:o60733] 8055.3 8331.1 1.03424
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] High confidence 5473.09 5887.45 1.07571
1471 40s ribosomal protein s8. [swissprot;acc:p09058] 5659.45 6087.55 1.07564
solute carrier family 7 (cationic amino acid transporter, y+ system), member 3. [refseq;acc:nm_032803] Low confidence 8113.2 8391.03 1.03424
1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] High confidence 5984.47 6435.42 1.07535
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Low confidence 8055.3 8331.1 1.03424
1473 calmegin precursor. [swissprot;acc:o14967] High confidence 5910.06 6355.08 1.0753
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, delta isoform (pp2a, b subunit, b' delta isoform) (pp2a, b subunit, b56 delta isoform) (pp2a, b subunit, pr61 delta isoform) (pp2a, b subunit, r5 delta isoform). [swissprot;acc:q14738] Low confidence 8055.3 8331.1 1.03424
1474 calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] High confidence 5910.06 6355.08 1.0753
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, gamma isoform (pp2a, b subunit, b' gamma isoform) (pp2a, b subunit, b56 gamma isoform) (pp2a, b subunit, pr61 gamma isoform) (pp2a, b subunit, r5 gamma isoform). [swissprot;acc:q13362] Low confidence 8055.3 8331.1 1.03424
1475 soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] High confidence 5910.06 6355.08 1.0753

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/