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 844 to 893 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
53	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Squared	Divided	0	0.458225	0.104379	4.39001
	transcription factor jun-b. [swissprot;acc:p17275]	Ranked		1	201.144	158.868	1.26611
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]			0	3284	4554.5	1.38688
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Squared	Subtracted		25325.5	29804.9	4479.4
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Measured			2230.13	1729.7	500.43
54	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked		1	185.678	245.247	59.569
	deltex 2. [refseq;acc:nm_020892]	Measured	Divided		1618.84	2651.88	1.63814
	exocyst complex component sec5. [swissprot;acc:q96kp1]		Subtracted		23316	19288.8	4027.2
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Divided	0	638.862	330.189	1.93484
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Rooted			14.8299	22.5463	1.52033
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Squared	Subtracted	1	173408	242989	69581
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		Divided		219048	129762	1.68808
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Rooted	Subtracted		137.446	120.823	16.623
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]			0	52.3183	44.8382	7.4801
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	Ranked			10793.5	14291.5	3498
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted	Divided	1	40.0958	58.7986	1.46645
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Squared		0	295.992	69.1109	4.28286
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]		Subtracted		25325.5	29804.9	4479.4
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Ranked	Divided		13884.4	19014.6	1.36949
	transcription factor jun-d. [swissprot;acc:p17535]			1	200.941	158.941	1.26425
	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	Measured	Subtracted	0	2230.13	1729.7	500.43
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]		Divided	1	1629.21	2662.12	1.63399
		Squared		0	468.221	113.017	4.14293
		Rooted			24.4683	16.281	1.50287
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Measured	Subtracted		2230.13	1729.7	500.43
	glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216]	Ranked		1	185.678	245.247	59.569
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	Divided		219048	129762	1.68808
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]		Subtracted		173408	242989	69581
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured	Divided	0	630.942	327.517	1.92644
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Rooted	Subtracted	1	137.446	120.823	16.623
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Ranked		0	22038	18578	3460
	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Measured		1	23303.1	19279.5	4023.6
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Squared		0	18175.2	13699.8	4475.4
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	Divided	1	41.6734	28.9323	1.44038
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked			320.927	254.434	1.26134
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Rooted	Subtracted	0	31.495	24.0263	7.4687
	sedlin. [swissprot;acc:o14582]	Ranked	Divided		22440	16388	1.36929
56	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	Squared	Subtracted		20324.3	15893.2	4431.1
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Rooted	Divided	1	41.6851	28.9509	1.43986
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Ranked	Subtracted		185.678	245.247	59.569
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		Divided		266.856	336.233	1.25998
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	Subtracted		173408	242989	69581
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Rooted			137.446	120.823	16.623
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared	Divided		219048	129762	1.68808
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Ranked	Subtracted	0	13975.7	10593.2	3382.5
		Rooted	Divided		11.2068	16.7658	1.49604
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Measured	Subtracted	1	20911	24908.5	3997.5
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Squared	Divided	0	15.4957	3.83288	4.04283
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Rooted	Subtracted		52.8301	45.6332	7.1969
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Ranked	Divided		22440	16388	1.36929

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.