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	Value Type	description	green	Interaction Map	red	Filtered	network_comparison

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Showing element 551 to 600 of 25824 in total

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

Rank	Value Type	description	green	red	network_comparison
138	Squared	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	468498	1.45156
	Rooted	musashi 1. [refseq;acc:nm_002442]	66.2416	54.9787	1.20486
139	Measured	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	2099.49	2759.61	1.31442
	Ranked	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	225.68	271.752	1.20415
	Squared	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	56211.1	81592.1	1.45153
	Rooted	nuclear protein ukp68. [refseq;acc:nm_024824]	66.2416	54.9787	1.20486
140	Measured	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	2100.27	2760.28	1.31425
	Ranked	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	49	59	1.20408
	Squared	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	56190.6	81527.6	1.45091
	Rooted	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	66.7332	55.6161	1.19989
141	Measured	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	5782.08	4405.4	1.3125
	Ranked	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	49	59	1.20408
	Squared	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	56188.5	81520.8	1.45084
	Rooted	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	66.7332	55.6161	1.19989
142	Measured	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	7090.37	9276.47	1.30832
	Ranked	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	49	59	1.20408
	Squared	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	56175.2	81478.9	1.45044
	Rooted	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	66.7332	55.6161	1.19989
143	Measured	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	7089.65	9275.1	1.30826
	Ranked	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	49	59	1.20408
	Squared	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	86848.2	124319	1.43145
	Rooted	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	66.7332	55.6161	1.19989
144	Measured	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	4362.61	3349.9	1.30231
	Ranked	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	319.651	265.686	1.20312
	Squared	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	86277.9	123324	1.42938
	Rooted	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	66.7332	55.6161	1.19989
145	Measured	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	12889.1	16771.5	1.30122
	Ranked	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	319.546	265.639	1.20293
	Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	442993	310840	1.42515
	Rooted	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	66.7332	55.6161	1.19989
146	Measured	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	8508.5	11068	1.30082
	Ranked	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	319.531	265.632	1.20291
	Squared	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	146848	103496	1.41888
	Rooted	huntingtin interacting protein c. [refseq;acc:nm_012272]	66.0298	55.0737	1.19894
147	Measured	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	8508.5	11068	1.30082
	Ranked	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	42.3003	50.7983	1.2009
	Squared	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	146848	103496	1.41888
	Rooted	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	50.4237	42.0574	1.19893
148	Measured	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	8508.5	11068	1.30082
	Ranked	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	247.559	296.677	1.19841
	Squared	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	146848	103496	1.41888
	Rooted	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	50.424	42.0577	1.19892
149	Measured	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	8508.5	11068	1.30082
	Ranked	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	170	142	1.19718
	Squared	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	146848	103496	1.41888
	Rooted	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	50.4323	42.0684	1.19882
150	Measured	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	8508.5	11068	1.30082
	Ranked	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	46	55	1.19565
	Squared	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	85473.4	121200	1.41799
	Rooted	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	53.0856	63.5827	1.19774

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.