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

Results: HTML CSV LaTeX

Showing element 1873 to 1922 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
118	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Squared	Subtracted	0	4121.56	5159.2	1037.64
	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Ranked	Divided		12049	14370.7	1.19269
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Measured	Subtracted	1	9275.1	7089.65	2185.45
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Ranked		0	3845	5699	1854
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Measured			324.442	593.094	268.652
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Rooted	Divided	1	50.3065	62.9788	1.2519
	methyltransferase like 2. [refseq;acc:nm_018396]	Measured		0	31	43	1.3871
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Rooted			9.1258	11.4849	1.25851
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Ranked		1	284.753	228.934	1.24382
		Rooted	Subtracted		37.2205	52.2064	14.9859
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Ranked			274.027	237.79	36.237
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured	Divided		21185	28492	1.34491
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Squared			210445	136779	1.53858
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]			0	240.689	124.83	1.92813
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted	Subtracted		32.6268	28.4118	4.215
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared		1	81888.8	56306.5	25582.3
119	40s ribosomal protein s29. [swissprot;acc:p30054]			0	5295.67	6326.82	1031.15
	60s ribosomal protein l7. [swissprot;acc:p18124]	Rooted			27.512	31.7228	4.2108
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Measured		1	12998.5	15138.2	2139.7
	adiponectin receptor 2. [refseq;acc:nm_024551]	Ranked			281.582	246.371	35.211
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared			81606.8	56215.8	25391
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Measured	Divided	0	633.85	460.2	1.37734
	exocyst complex component sec5. [swissprot;acc:q96kp1]	Squared		1	210335	136716	1.53848
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Ranked		0	3609	4302.5	1.19216
	methyltransferase like 2. [refseq;acc:nm_018396]	Squared			0.227456	0.437633	1.92403
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Measured		1	21185	28492	1.34491
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	Ranked			318.982	259.004	1.23157
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]		Subtracted	0	7739.47	9580.95	1841.48
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Rooted	Divided		4.72248	5.90479	1.25036
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]		Subtracted	1	63.6507	48.7127	14.938
	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807]		Divided		50.3247	62.9892	1.25166
	ubiquitin protein ligase. [refseq;acc:nm_130466]	Measured	Subtracted	0	620	352.75	267.25
120	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Squared			4225.7	5255.44	1029.74
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Rooted	Divided		22.9115	28.547	1.24597
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Squared	Subtracted	1	81592.1	56211.1	25381
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Rooted			40.081	25.1546	14.9264
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Measured	Divided		5136.78	6895.98	1.34247
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Rooted			50.3333	62.9942	1.25154
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked	Subtracted		227.199	192.715	34.484
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Squared	Divided		210199	136638	1.53836
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Ranked			269.278	327.709	1.21699
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]			0	5797	4873	1.18962
		Rooted	Subtracted		29.5635	33.7491	4.1856
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Measured		1	4932.27	7033.29	2101.02
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]		Divided	0	494.417	359.631	1.37479
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Ranked	Subtracted		11438	13277.1	1839.1
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Squared	Divided		6.45653	12.2937	1.90407
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Measured	Subtracted		817.81	551.434	266.376
121	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]		Divided		19.6667	14.3333	1.3721
	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Squared	Subtracted		4224.07	5253.37	1029.3

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.