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	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	description	Value Type	red	network_comparison	green
126	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
127	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		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
128	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
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		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
130	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
131	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
132	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
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted	44.963	1.22451	55.0576
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Ranked	350	1.2069	290
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	23421.5	1.33225	17580.4
	gbp protein isoform a. [refseq;acc:nm_017870]	Squared	1182.25	1.46039	1726.55
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Rooted	45.4558	1.22316	55.5995
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked	350	1.2069	290
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	1.2218	54.7964
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured	21785.2	1.32626	16426.1
	p66 alpha. [refseq;acc:nm_017660]	Squared	81888.8	1.45434	56306.5
135	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Rooted	54.935	1.21253	66.6101
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured	21785.2	1.32626	16426.1
	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked	350	1.2069	290
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Squared	81888.8	1.45434	56306.5
136	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted	41.8357	1.21061	50.6469
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	350	1.2069	290
	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	1.31556	4763.34
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared	81888.8	1.45434	56306.5
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	1.31556	4763.34
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	81606.8	1.45167	56215.8
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted	54.9787	1.20486	66.2416
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked	350	1.2069	290
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	2755.15	1.31555	2094.3
	musashi 1. [refseq;acc:nm_002442]	Rooted	54.9787	1.20486	66.2416

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.