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	green	red	network_comparison

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Showing element 501 to 550 of 12912 in total

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

Rank	description	Value Type	green	red	network_comparison
126	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	114	94	1.21277
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	18164.9	24250	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	75.1387	60.9342	1.23311
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	124480	189976	1.52616
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		58423.3	88432.6	1.51365
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	75.094	60.9353	1.23236
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	114	94	1.21277
	transcription factor jun-d. [swissprot;acc:p17535]	Measured	7523.39	5638.2	1.33436
128	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	114	94	1.21277
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	5810.82	4355.61	1.3341
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	58155.8	87787.3	1.50952
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	39.0445	48.0515	1.23069
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		66.7323	54.2343	1.23044
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured	5811.49	4358.13	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked	114	94	1.21277
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	118639	178263	1.50257
130	44050 protein. [refseq;acc:nm_178832]		99628.4	148058	1.4861
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured	2978.53	2234.68	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	67.5701	55.1026	1.22626
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	114	94	1.21277
131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	2978.57	2234.73	1.33285
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted	67.5537	55.1113	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	99628.4	148058	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	242.562	294.053	1.21228
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	24466.8	36359.2	1.48606
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	2980.35	2236.61	1.33253
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted	55.0576	44.963	1.22451
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked	290	350	1.2069
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	17580.4	23421.5	1.33225
	gbp protein isoform a. [refseq;acc:nm_017870]	Squared	1726.55	1182.25	1.46039
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted	55.5995	45.4558	1.22316
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	290	350	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	54.7964	44.849	1.2218
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured	16426.1	21785.2	1.32626
	p66 alpha. [refseq;acc:nm_017660]	Squared	56306.5	81888.8	1.45434
135	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Rooted	66.6101	54.935	1.21253
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured	16426.1	21785.2	1.32626
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked	290	350	1.2069
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Squared	56306.5	81888.8	1.45434
136	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted	50.6469	41.8357	1.21061
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	290	350	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	4763.34	3620.77	1.31556
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared	56306.5	81888.8	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	4763.34	3620.77	1.31556
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	56215.8	81606.8	1.45167
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted	66.2416	54.9787	1.20486
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked	290	350	1.2069
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	2094.3	2755.15	1.31555
	musashi 1. [refseq;acc:nm_002442]	Rooted	66.2416	54.9787	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.