Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 427 to 476 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
54	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Rooted	0	14.8299	22.5463	1.52033
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Squared	1	219048	129762	1.68808
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Rooted	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
	syntaxin 10 (syn10). [swissprot;acc:o60499]	Ranked	0	13884.4	19014.6	1.36949
	transcription factor jun-d. [swissprot;acc:p17535]	Ranked	1	200.941	158.941	1.26425
55	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Measured	1	1629.21	2662.12	1.63399
		Squared	0	468.221	113.017	4.14293
		Rooted	0	24.4683	16.281	1.50287
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Squared	1	219048	129762	1.68808
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Measured	0	630.942	327.517	1.92644
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	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	1	320.927	254.434	1.26134
	sedlin. [swissprot;acc:o14582]	Ranked	0	22440	16388	1.36929
56	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Rooted	1	41.6851	28.9509	1.43986
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Ranked		266.856	336.233	1.25998
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Squared		219048	129762	1.68808
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Rooted	0	11.2068	16.7658	1.49604
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Squared		15.4957	3.83288	4.04283
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Ranked		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
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]			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
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Ranked	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
	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]	Rooted		41.6879	28.9554	1.43973
58	40s ribosomal protein s26. [swissprot;acc:p02383]	Measured	0	150.741	81.2233	1.85588
	dead-box protein. [refseq;acc:nm_018665]	Ranked	0	10628.3	14486	1.36296
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Ranked	1	266.863	336.191	1.25979
	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	Measured		1631.67	2664.55	1.63302
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Squared		219048	129762	1.68808
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Squared	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
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Rooted	0	11.6322	7.84538	1.48268
59	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Squared		57.8417	218.049	3.76975
	f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755]	Measured		150.673	279.24	1.85328
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Ranked		15863.6	11662.3	1.36025
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Ranked	1	266.863	336.19	1.25978
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Squared		219048	129762	1.68808
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Measured		1631.67	2664.55	1.63302
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Rooted	0	4.28588	6.23127	1.45391
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Rooted	1	37.2205	52.2064	1.40262
60	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	1	4489.19	2765.82	1.6231
	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Measured	0	47.4756	87.5499	1.8441
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Ranked	0	11761	15924	1.35397
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Ranked	1	266.864	336.184	1.25976

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.

- http://analysis.yellowcouch.org/