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

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Showing element 351 to 400 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
44	Rooted	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Divided	40.5691	25.4263	1.59556
		protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Subtracted	60.8692	77.7165	16.8473
45	Measured	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Divided	1926.69	1056.02	1.82448
		protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Subtracted	27642.5	22440.4	5202.1
	Ranked	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]		332.874	267.246	65.628
		protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Divided	204.641	161.051	1.27066
	Squared	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		129597	73157.5	1.77148
		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Subtracted	110342	184298	73956
	Rooted	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		60.875	77.7152	16.8402
		guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Divided	40.081	25.1546	1.59339
46	Measured	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Subtracted	24896.4	20431.7	4464.7
		neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	779.167	1390.33	1.78438
	Ranked	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		204.642	161.068	1.27053
		neuralized-like. [refseq;acc:nm_004210]	Subtracted	332.326	266.948	65.378
	Squared	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Divided	129597	73157.5	1.77148
		poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Subtracted	210445	136779	73666
	Rooted	deltex 2. [refseq;acc:nm_020892]	Divided	27.634	43.9629	1.5909
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	137.446	120.823	16.623
47	Measured	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Divided	779.167	1390.33	1.78438
		trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	24896.4	20431.7	4464.7
	Ranked	gbp protein isoform a. [refseq;acc:nm_017870]	Divided	325.586	256.492	1.26938
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Subtracted	350	290	60
	Squared	exocyst complex component sec5. [swissprot;acc:q96kp1]		210335	136716	73619
		ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Divided	98517.9	56927.2	1.73059
	Rooted	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]		27.7078	44.017	1.58861
		hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	137.446	120.823	16.623
48	Measured	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Divided	779.167	1390.33	1.78438
		wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	24806.9	20369.9	4437
	Ranked	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	65.4586	83.0461	1.26868
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Subtracted	350	290	60
	Squared	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Divided	6300.2	10703.5	1.69891
		poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Subtracted	210199	136638	73561
	Rooted	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]		137.446	120.823	16.623
		t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Divided	27.7254	44.0299	1.58807
49	Measured	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Subtracted	24806.9	20369.9	4437
		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided	779.167	1390.33	1.78438
	Ranked	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]		133	105	1.26667
		dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Subtracted	350	290	60
	Squared	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Divided	28994.2	17134.8	1.69212
		cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	Subtracted	201896	131906	69990
	Rooted	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Divided	27.7254	44.0299	1.58807
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	137.446	120.823	16.623
50	Measured	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]		24473.9	20127.8	4346.1
		neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Divided	779.167	1390.33	1.78438
	Ranked	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]		133	105	1.26667
		cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Subtracted	350	290	60
	Squared	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		173408	242989	69581
		putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Divided	28994.2	17134.8	1.69212
	Rooted	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]		27.7254	44.0299	1.58807
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Subtracted	137.446	120.823	16.623

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.