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

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Showing element 501 to 550 of 25824 in total

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

Rank	description	Value Type	red	green	network_comparison
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	94	114	1.21277
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	24250	18164.9	1.33499
	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	75.1387	1.23311
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	189976	124480	1.52616
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		88432.6	58423.3	1.51365
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	60.9353	75.094	1.23236
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	94	114	1.21277
	transcription factor jun-d. [swissprot;acc:p17535]	Measured	5638.2	7523.39	1.33436
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	94	114	1.21277
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	4355.61	5810.82	1.3341
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	87787.3	58155.8	1.50952
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	48.0515	39.0445	1.23069
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		54.2343	66.7323	1.23044
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured	4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked	94	114	1.21277
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	178263	118639	1.50257
130	44050 protein. [refseq;acc:nm_178832]		148058	99628.4	1.4861
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured	2234.68	2978.53	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	55.1026	67.5701	1.22626
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	94	114	1.21277
131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	2234.73	2978.57	1.33285
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted	55.1113	67.5537	1.22577
	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	99628.4	1.4861
	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	242.562	1.21228
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	36359.2	24466.8	1.48606
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	2236.61	2980.35	1.33253
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted	44.963	55.0576	1.22451
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked	350	290	1.2069
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	23421.5	17580.4	1.33225
	gbp protein isoform a. [refseq;acc:nm_017870]	Squared	1182.25	1726.55	1.46039
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted	45.4558	55.5995	1.22316
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	350	290	1.2069
134	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Rooted	44.849	54.7964	1.2218
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured	21785.2	16426.1	1.32626
	p66 alpha. [refseq;acc:nm_017660]	Squared	81888.8	56306.5	1.45434
135	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Rooted	54.935	66.6101	1.21253
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured	21785.2	16426.1	1.32626
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked	350	290	1.2069
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Squared	81888.8	56306.5	1.45434
136	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted	41.8357	50.6469	1.21061
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	350	290	1.2069
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Measured	3620.77	4763.34	1.31556
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared	81888.8	56306.5	1.45434
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Measured	3620.77	4763.34	1.31556
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	81606.8	56215.8	1.45167
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted	54.9787	66.2416	1.20486
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked	350	290	1.2069
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	2755.15	2094.3	1.31555
	musashi 1. [refseq;acc:nm_002442]	Rooted	54.9787	66.2416	1.20486

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.