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 873 to 922 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
55	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
	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]	Measured		1	1631.67	2664.55	1.63302
	tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]			0	271.484	142.981	1.89874
	udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]		Subtracted		2230.13	1729.7	500.43
57	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]		Divided		270.264	142.417	1.89769
	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Squared			0.849445	3.43037	4.03837
	dead-box protein. [refseq;acc:nm_018665]	Rooted			16.237	10.8929	1.4906
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Ranked		1	266.856	336.233	1.25998
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	Subtracted		173408	242989	69581
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Ranked	Divided	0	8152.55	11134.8	1.36581
	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Measured		1	1631.67	2664.55	1.63302
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Squared			219048	129762	1.68808
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Rooted	Subtracted		137.446	120.823	16.623
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Ranked			185.678	245.247	59.569
	nanos (fragment). [sptrembl;acc:q8wy41]	Rooted		0	19.4165	12.2882	7.1283
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]		Divided	1	41.6879	28.9554	1.43973
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Measured	Subtracted		20911	24908.5	3997.5
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Squared		0	82695.1	87060.9	4365.8
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Ranked			19048	22389	3341
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Measured			2230.13	1729.7	500.43
58	40s ribosomal protein s26. [swissprot;acc:p02383]		Divided		150.741	81.2233	1.85588
	dead-box protein. [refseq;acc:nm_018665]	Ranked			10628.3	14486	1.36296
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]		Subtracted	1	185.678	245.247	59.569
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]		Divided		266.863	336.191	1.25979
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Measured	Subtracted	0	11512.3	12011.7	499.4
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]		Divided	1	1631.67	2664.55	1.63302
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared			219048	129762	1.68808
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	Subtracted		137.446	120.823	16.623
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Squared	Divided	0	129.158	488.851	3.78491
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Rooted		1	41.6969	28.9696	1.43933

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.