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 1900 to 1949 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
119	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Ranked	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
	alpha crystallin a chain. [swissprot;acc:p02489]		Divided		1.27019	2.40686	1.89488
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]		Subtracted	1	81527.6	56190.6	25337
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Ranked	Divided		269.254	327.655	1.2169
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Rooted			50.339	62.9975	1.25147
	jun dimerization protein. [refseq;acc:nm_130469]	Measured	Subtracted		4932.27	7033.29	2101.02
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Ranked		0	18241.7	16405	1836.7
	myosin vi. [swissprot;acc:q9um54]	Rooted	Divided		17.3551	14.0846	1.2322
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Ranked	Subtracted	1	227.202	192.823	34.379
	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	Measured		0	874	1139	265
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Rooted			13.2903	17.4395	4.1492
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]			1	63.6205	48.8838	14.7367
	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873]	Squared	Divided		199594	130021	1.53509
	transcription factor jun-b. [swissprot;acc:p17275]	Measured			5579.18	7488.4	1.3422
	zinc finger protein 232. [swissprot;acc:q9uny5]	Ranked		0	11523.7	13686.9	1.18772
122	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Squared	Subtracted		4214.44	5226.4	1011.96
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Measured			2198.47	1933.94	264.53
	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Squared	Divided	1	201896	131906	1.53061
	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Ranked	Subtracted		199.949	234.187	34.238
	fos-related antigen 2. [swissprot;acc:p15408]	Measured			4941.95	7037.11	2095.16
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Squared			81520.8	56188.5	25332.3
	high-mobility group 20a. [refseq;acc:nm_018200]	Measured	Divided		5140.14	6893.53	1.34112
	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]	Rooted	Subtracted		60.9342	75.1387	14.2045
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Ranked		0	12384.7	10549.4	1835.3
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Rooted	Divided		9.00325	7.33715	1.22708
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	Ranked		1	269.248	327.642	1.21688
	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Measured		0	107	78	1.37179
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Rooted	Subtracted		13.2903	17.4395	4.1492

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.