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

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Showing element 501 to 550 of 12912 in total

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

Rank	Value Type	description	red	network_comparison	green
126	Measured	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	24250	1.33499	18164.9
	Ranked	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	94	1.21277	114
	Squared	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	189976	1.52616	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]	60.9342	1.23311	75.1387
127	Measured	transcription factor jun-d. [swissprot;acc:p17535]	5638.2	1.33436	7523.39
	Ranked	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	94	1.21277	114
	Squared	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	88432.6	1.51365	58423.3
	Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	60.9353	1.23236	75.094
128	Measured	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	4355.61	1.3341	5810.82
	Ranked	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	94	1.21277	114
	Squared	pnas-18. [sptrembl;acc:q9bzu3]	87787.3	1.50952	58155.8
	Rooted	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	48.0515	1.23069	39.0445
129	Measured	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	4358.13	1.33348	5811.49
	Ranked	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	94	1.21277	114
	Squared	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	178263	1.50257	118639
	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	54.2343	1.23044	66.7323
130	Measured	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	2234.68	1.33287	2978.53
	Ranked	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	94	1.21277	114
	Squared	44050 protein. [refseq;acc:nm_178832]	148058	1.4861	99628.4
	Rooted	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	55.1026	1.22626	67.5701
131	Measured	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	2234.73	1.33285	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]	294.053	1.21228	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]	148058	1.4861	99628.4
	Rooted	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	55.1113	1.22577	67.5537
132	Measured	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	2236.61	1.33253	2980.35
	Ranked	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	350	1.2069	290
	Squared	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	36359.2	1.48606	24466.8
	Rooted	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	44.963	1.22451	55.0576
133	Measured	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	23421.5	1.33225	17580.4
	Ranked	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	350	1.2069	290
	Squared	gbp protein isoform a. [refseq;acc:nm_017870]	1182.25	1.46039	1726.55
	Rooted	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	45.4558	1.22316	55.5995
134	Measured	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	21785.2	1.32626	16426.1
	Ranked	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	350	1.2069	290
	Squared	p66 alpha. [refseq;acc:nm_017660]	81888.8	1.45434	56306.5
	Rooted	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	44.849	1.2218	54.7964
135	Measured	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	21785.2	1.32626	16426.1
	Ranked	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	350	1.2069	290
	Squared	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	81888.8	1.45434	56306.5
	Rooted	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	54.935	1.21253	66.6101
136	Measured	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]	3620.77	1.31556	4763.34
	Ranked	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	350	1.2069	290
	Squared	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	81888.8	1.45434	56306.5
	Rooted	adiponectin receptor 2. [refseq;acc:nm_024551]	41.8357	1.21061	50.6469
137	Measured	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]	3620.77	1.31556	4763.34
	Ranked	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	350	1.2069	290
	Squared	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	81606.8	1.45167	56215.8
	Rooted	musashi 2 isoform a. [refseq;acc:nm_138962]	54.9787	1.20486	66.2416
138	Measured	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	2755.15	1.31555	2094.3
	Ranked	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	194.372	1.20493	234.204

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.