MK5 Microarray Data

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

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Showing element 2308 to 2357 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
2308	protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817]	215.543	214.459	1.00505
2309	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	215.542
2310	ubiquitin. [swissprot;acc:p02248]	216.617	215.529
2311	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694]	215.542	214.459
2312	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612]
2313	camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323]	215.529	214.449	1.00504
2314	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669]	194.743	195.708	1.00496
2315	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	194.825	195.787	1.00494
2316	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	217.241	218.311	1.00493
2317	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743]	194.834	195.794
2318	sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]
2319	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]	194.842	195.8	1.00492
2320	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	219.292	218.218
2321	tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801]	203.909	202.925	1.00485
2322	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	236.023	234.905	1.00476
2323	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776]	192.773	193.691
2324	proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [swissprot;acc:p20618]	212.129	211.129	1.00474
2325	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	221.728	220.685	1.00473
2326	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	220.076	219.05	1.00468
2327	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	217.413	218.426	1.00466
2328	xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	209.326	208.357	1.00465
2329	26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	217.112	218.116	1.00462
2330	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9]	214.213	213.235	1.00459
2331	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	229.258	230.294	1.00452
2332	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
2333	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
2334	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
2335	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
2336	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
2337	homeobox protein dlx-2. [swissprot;acc:q07687]
2338	homeobox protein dlx-5. [swissprot;acc:p56178]
2339	fetal brain protein 239 (239fb). [swissprot;acc:q15777]
2340	homeobox protein dlx-3. [swissprot;acc:o60479]
2341	activated p21cdc42hs kinase. [refseq;acc:nm_005781]
2342	mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
2343	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]	212.222	211.27	1.00451
2344	kccr13l. [refseq;acc:nm_139179]	219.878	218.893	1.0045
2345	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
2346	serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6]	217.057	218.03	1.00448
2347	serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956]
2348	glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406]
2349	fibulin-1 precursor. [swissprot;acc:p23142]	192.348	191.503	1.00441
2350	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	209.811	210.733	1.00439
2351	synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	214.223	213.289	1.00438
2352	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656]	215.088	214.155	1.00436
2353	electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	182.232	183.027
2354	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670]	215.078	214.148	1.00434
2355	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	217.232	218.162	1.00428
2356	importin 4. [refseq;acc:nm_024658]	220.921	221.863	1.00426
2357	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	198.181	197.346	1.00423

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.