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

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Showing element 1001 to 1050 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	Value Type	description	network_comparison	red	green
126	Divided	Measured	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1.33499	24250	18164.9
		Ranked	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	1.21277	94	114
		Squared	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	1.52616	189976	124480
		Rooted	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]	1.23311	60.9342	75.1387
	Subtracted	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	1944	450.5	2394.5
		Ranked	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	33.45	285.684	252.234
		Squared	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]	24646	71387.4	96033.4
		Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	14.1587	60.9353	75.094
127	Divided	Measured	transcription factor jun-d. [swissprot;acc:p17535]	1.33436	5638.2	7523.39
		Ranked	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	1.21277	94	114
		Squared	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	1.51365	88432.6	58423.3
		Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	1.23236	60.9353	75.094
	Subtracted	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1944	450.5	2394.5
		Ranked	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	33.45	285.684	252.234
		Squared	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	24645.6	71386.9	96032.5
		Rooted	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	13.58	153.191	166.771
128	Divided	Measured	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	1.3341	4355.61	5810.82
		Ranked	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	1.21277	94	114
		Squared	pnas-18. [sptrembl;acc:q9bzu3]	1.50952	87787.3	58155.8
		Rooted	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	1.23069	48.0515	39.0445
	Subtracted	Measured	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	1940	11004.2	12944.2
		Ranked	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	33.45	285.684	252.234
		Squared	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	24618.5	71346.6	95965.1
		Rooted	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	13.3216	54.6527	67.9743
129	Divided	Measured	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	1.33348	4358.13	5811.49
		Ranked	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	1.21277	94	114
		Squared	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	1.50257	178263	118639
		Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	1.23044	54.2343	66.7323
	Subtracted	Measured	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	1928	15274.9	13346.9
		Ranked	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	33.45	285.684	252.234
		Squared	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	24426.5	71062.4	95488.9
		Rooted	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	13.2852	54.6625	67.9477
130	Divided	Measured	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	1.33287	2234.68	2978.53
		Ranked	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	1.21277	94	114
		Squared	44050 protein. [refseq;acc:nm_178832]	1.4861	148058	99628.4
		Rooted	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	1.22626	55.1026	67.5701
	Subtracted	Measured	p66 alpha. [refseq;acc:nm_017660]	1927.9	12839	10911.1
		Ranked	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	33.324	242.735	276.059
		Squared	calsyntenin-1 precursor. [swissprot;acc:o94985]	24426.5	71062.4	95488.9
		Rooted	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	13.218	144.606	157.824
131	Divided	Measured	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	1.33285	2234.73	2978.57
		Ranked	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	1.21228	294.053	242.562
		Squared	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	1.4861	148058	99628.4
		Rooted	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	1.22577	55.1113	67.5537
	Subtracted	Measured	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	1927.9	12839	10911.1
		Ranked	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	33.3	242.718	276.018
		Squared	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	24426.5	71062.4	95488.9
		Rooted	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	13.218	144.606	157.824
132	Divided	Measured	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	1.33253	2236.61	2980.35
		Ranked	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	1.2069	350	290

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.