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 2908 to 2957 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1454 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
1463 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] 5672.2 6103.92 1.07611
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Subtracted 5692.53 6134.64 442.11
1464 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 4757.46 5198.91 441.45
zasp protein (fragment). [sptrembl;acc:q9y4z3] Divided 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
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Subtracted 4757.46 5198.91 441.45
1466 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] Divided 6523.17 7019.44 1.07608
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Subtracted 4757.46 5198.91 441.45
1467 p47 protein isoform a. [refseq;acc:nm_016143] Divided 6444.4 6932.39 1.07572
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Subtracted 4757.46 5198.91 441.45
1468 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Divided 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]
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Subtracted 4757.46 5198.91 441.45
1470 homeobox protein dlx-2. [swissprot;acc:q07687]
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Divided 5473.09 5887.45 1.07571
1471 40s ribosomal protein s8. [swissprot;acc:p09058] 5659.45 6087.55 1.07564
homeobox protein dlx-5. [swissprot;acc:p56178] Subtracted 4757.46 5198.91 441.45
1472 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Divided 5984.47 6435.42 1.07535
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Subtracted 4757.46 5198.91 441.45
1473 calmegin precursor. [swissprot;acc:o14967] Divided 5910.06 6355.08 1.0753
homeobox protein dlx-3. [swissprot;acc:o60479] Subtracted 4757.46 5198.91 441.45
1474 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] Divided 5910.06 6355.08 1.0753
1475 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Subtracted 4757.46 5198.91 441.45
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Divided 5910.06 6355.08 1.0753
1476 rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799]
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Subtracted 6078.43 6519.6 441.17
1477 malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 6617.91 441.09
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 3687.37 3429.37 1.07523
1478 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 5659.22 6084.68 1.07518
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Subtracted 6176.82 6617.91 441.09
1479 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Divided 5787.03 6221.72 1.07511

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/