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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Gene	Network Comparison Type	red	green	Value Type	Rank	Interaction Map	description	Filtered	network_comparison

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Showing element 2368 to 2417 of 3228 in total

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

red	green	Rank	description	network_comparison
6203.95	6360.24	2516	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223]	1.02519
6203.96		2517	eh-domain containing protein 2. [swissprot;acc:q9nzn4]
6204.15	6360.27	2518	sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422]	1.02516
6204.25	6360.69	2513	reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799]	1.02521
6205.14	6359.44	2528	reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3]	1.02487
6207.57	6718.7	1285	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	1.08234
6209.77	6501.99	2246	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	1.04706
6210.51	6693.49	1406	ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477]	1.07777
6212.98	6655.12	1612	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	1.07116
6213.27	6659.39	1578	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]	1.0718
6213.51	6785.04	1083	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	1.09198
6215.55	6613.46	1847	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	1.06402
6216.12	6693.38	1441	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818]	1.07678
6216.13	6693.13	1442	proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3]	1.07674
6218.34	6575.81	2027	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584]	1.05749
6221.22	6727.77	1311	exocyst complex component sec8. [swissprot;acc:q96a65]	1.08142
6221.35	6672.51	1563	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]	1.07252
6222.4	6665.83	1610	eif-5a2 protein. [refseq;acc:nm_020390]	1.07126
6222.8	6723.54	1326	mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620]	1.08047
6227.87	7012.9	620	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	1.12605
6228.39	7013.19	623	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	1.126
		624	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
		625	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
		626	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]
		627	limkain b1. [refseq;acc:nm_019081]
		628	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
		629	cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
		630	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
		631	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042]
		632	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
		633	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]
		634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
6228.42	7013.21	622	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]
6228.97	7013.53	635	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	1.12595
6229.16	6742.79	1283	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354]	1.08246
6229.69	6829.58	988	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	1.0963
6230.21	6608.64	1945	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	1.06074
		1946	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
		1948	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]
		1949	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
6230.38	6744.35	1282	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570]	1.08249
6230.49	6744.5	1281	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736]	1.0825
6230.94	7168.2	436	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	1.15042
6231.31	6933.9	762	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	1.11275
6237.83	6400.74	2505	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	1.02612
6239.69	6378.35	2544	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044]	1.02222
6245.32	6534.23	2257	sr rich protein. [refseq;acc:nm_032870]	1.04626
6251.32	6774.12	1258	glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	1.08363
6251.91	7192.08	440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	1.15038
6251.96	7192.13	441	grancalcin. [swissprot;acc:p28676]

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.