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	green	network_comparison

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Showing element 532 to 581 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
133	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
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared	468498	322755	1.45156
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Ranked	194.372	234.204	1.20493
139	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]		271.752	225.68	1.20415
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Squared	81592.1	56211.1	1.45153
	nuclear protein ukp68. [refseq;acc:nm_024824]	Rooted	54.9787	66.2416	1.20486
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Measured	2759.61	2099.49	1.31442
140	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Squared	81527.6	56190.6	1.45091
	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]	Rooted	55.6161	66.7332	1.19989
	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]	Measured	2760.28	2100.27	1.31425
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Ranked	59	49	1.20408
141	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Squared	81520.8	56188.5	1.45084
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Ranked	59	49	1.20408
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted	55.6161	66.7332	1.19989
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Measured	4405.4	5782.08	1.3125
142	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Squared	81478.9	56175.2	1.45044
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Measured	9276.47	7090.37	1.30832
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Rooted	55.6161	66.7332	1.19989
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Ranked	59	49	1.20408
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Measured	9275.1	7089.65	1.30826
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Rooted	55.6161	66.7332	1.19989
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Squared	124319	86848.2	1.43145
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Ranked	265.686	319.651	1.20312
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Measured	3349.9	4362.61	1.30231
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Squared	123324	86277.9	1.42938
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Rooted	55.6161	66.7332	1.19989
145	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	310840	442993	1.42515
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Ranked	265.639	319.546	1.20293
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	16771.5	12889.1	1.30122
146	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]		11068	8508.5	1.30082

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.