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

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Showing element 782 to 831 of 3228 in total

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

green	Rank	description	network_comparison	red
192.715	170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	1.17894	227.199
192.823	171	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	1.17829	227.202
192.849	1174	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579]	1.02599	187.964
192.922	2577	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	1.00154	192.625
192.977	1558	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	1.01655	196.171
192.996	1555	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	1.01656	196.192
	1556	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
	1557	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
	1559	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1.01655	196.191
193.018	1554	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	1.01656	196.215
193.021	560	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	1.06589	205.74
193.056	173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	1.17599	227.032
193.183	561	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]	1.06578	205.89
193.38	1900	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	1.01034	191.401
193.385	1903	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]		191.406
193.387	1907	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]		191.408
193.389	1906	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]		191.41
193.39	1901	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]		191.411
	1902	lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
	1905	disrupter of silencing 10. [refseq;acc:nm_020368]
193.394	1908	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]		191.415
193.404	1904	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975]		191.424
193.46	2556	chromodomain y-like protein 2. [refseq;acc:nm_152342]	1.00177	193.119
193.467	2552	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	1.0018	193.12
	2553	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
	2554	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]
193.555	2428	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	1.00355	192.871
	2429	esterase d (ec 3.1.1.1). [swissprot;acc:p10768]
193.691	2323	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776]	1.00476	192.773
193.706	2408	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	1.00362	194.407
	2409	lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]
	2410	lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]
	2411	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]
	2412	lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]
193.871	2508	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	1.00247	194.349
194.105	2404	acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424]	1.0037	193.389
194.22	2254	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	1.00598	193.065
194.262	546	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	1.06671	207.222
194.328	2642	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	1.00119	194.097
	2643	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
	2644	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
	2645	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
194.346	547	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	1.06645	207.26
	548	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]
	549	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
	550	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]
	552	crk-like protein. [swissprot;acc:p46109]
	553	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519]
	554	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]
	555	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]

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.