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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Network Comparison Type	description	Value Type	red	network_comparison	green
126	Divided	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	94	1.21277	114
		cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	24250	1.33499	18164.9
		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	60.9342	1.23311	75.1387
		serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	189976	1.52616	124480
	Subtracted	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]		71387.4	24646	96033.4
		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]	Ranked	285.684	33.45	252.234
		high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	60.9353	14.1587	75.094
		rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	450.5	1944	2394.5
127	Divided	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared	88432.6	1.51365	58423.3
		high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	60.9353	1.23236	75.094
		putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	94	1.21277	114
		transcription factor jun-d. [swissprot;acc:p17535]	Measured	5638.2	1.33436	7523.39
	Subtracted	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked	285.684	33.45	252.234
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Rooted	153.191	13.58	166.771
		lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	71386.9	24645.6	96032.5
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	450.5	1944	2394.5
128	Divided	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	94	1.21277	114
		luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	4355.61	1.3341	5810.82
		pnas-18. [sptrembl;acc:q9bzu3]	Squared	87787.3	1.50952	58155.8
		tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	48.0515	1.23069	39.0445
	Subtracted	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Squared	71346.6	24618.5	95965.1
		nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Rooted	54.6527	13.3216	67.9743
		presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Ranked	285.684	33.45	252.234
		t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Measured	11004.2	1940	12944.2
129	Divided	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	54.2343	1.23044	66.7323
		luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured	4358.13	1.33348	5811.49
		neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked	94	1.21277	114
		pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	178263	1.50257	118639
	Subtracted	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Ranked	285.684	33.45	252.234
		nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Rooted	54.6625	13.2852	67.9477
		protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Measured	15274.9	1928	13346.9
		translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Squared	71062.4	24426.5	95488.9
130	Divided	44050 protein. [refseq;acc:nm_178832]		148058	1.4861	99628.4
		forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured	2234.68	1.33287	2978.53
		formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	55.1026	1.22626	67.5701
		protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	94	1.21277	114
	Subtracted	calsyntenin-1 precursor. [swissprot;acc:o94985]	Squared	71062.4	24426.5	95488.9
		p66 alpha. [refseq;acc:nm_017660]	Measured	12839	1927.9	10911.1
		palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Ranked	242.735	33.324	276.059
		ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Rooted	144.606	13.218	157.824
131	Divided	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	2234.73	1.33285	2978.57
		huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted	55.1113	1.22577	67.5537
		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]	Squared	148058	1.4861	99628.4
		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]	Ranked	294.053	1.21228	242.562
	Subtracted	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]		242.718	33.3	276.018
		ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Rooted	144.606	13.218	157.824
		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]	Squared	71062.4	24426.5	95488.9
		transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Measured	12839	1927.9	10911.1
132	Divided	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	36359.2	1.48606	24466.8
		forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	2236.61	1.33253	2980.35

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.