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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 430 to 479 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
54	soluble liver antigen/liver pancreas antigen. [source:refseq;acc:nm_153825]	Squared	0	295.992	69.1109	4.28286	
54	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Ranked	0	13884.4	19014.6	1.36949	
54	transcription factor jun-d. [source:swissprot;acc:p17535]	Ranked	1	200.941	158.941	1.26425	
55	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Measured	1	1629.21	2662.12	1.63399	
55	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Squared	0	468.221	113.017	4.14293	
55	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Rooted	0	24.4683	16.281	1.50287	
55	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Squared	1	219048	129762	1.68808	
55	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Measured	0	630.942	327.517	1.92644	
55	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Rooted	1	41.6734	28.9323	1.44038	
55	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Ranked	1	320.927	254.434	1.26134	
55	sedlin. [source:swissprot;acc:o14582]	Ranked	0	22440	16388	1.36929	
56	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Rooted	1	41.6851	28.9509	1.43986	
56	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Ranked	1	266.856	336.233	1.25998	
56	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Squared	1	219048	129762	1.68808	
56	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [source:refseq;acc:nm_003981]	Rooted	0	11.2068	16.7658	1.49604	
56	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]	Squared	0	15.4957	3.83288	4.04283	
56	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Ranked	0	22440	16388	1.36929	
56	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	Measured	1	1631.67	2664.55	1.63302	
56	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Measured	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). [source:swissprot;acc:p17643]	Measured	0	270.264	142.417	1.89769	
57	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). [source:swissprot;acc:p45954]	Squared	0	0.849445	3.43037	4.03837	
57	dead-box protein. [source:refseq;acc:nm_018665]	Rooted	0	16.237	10.8929	1.4906	
57	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Ranked	1	266.856	336.233	1.25998	
57	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	Ranked	0	8152.55	11134.8	1.36581	
57	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	Measured	1	1631.67	2664.55	1.63302	
57	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Squared	1	219048	129762	1.68808	
57	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. [source:refseq;acc:nm_004980]	Rooted	1	41.6879	28.9554	1.43973	
58	40s ribosomal protein s26. [source:swissprot;acc:p02383]	Measured	0	150.741	81.2233	1.85588	
58	dead-box protein. [source:refseq;acc:nm_018665]	Ranked	0	10628.3	14486	1.36296	
58	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	Ranked	1	266.863	336.191	1.25979	
58	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	Measured	1	1631.67	2664.55	1.63302	
58	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Squared	1	219048	129762	1.68808	
58	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Squared	0	129.158	488.851	3.78491	
58	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Rooted	1	41.6969	28.9696	1.43933	
58	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]	Rooted	0	11.6322	7.84538	1.48268	
59	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Squared	0	57.8417	218.049	3.76975	
59	f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	Measured	0	150.673	279.24	1.85328	
59	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	Ranked	0	15863.6	11662.3	1.36025	
59	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	Ranked	1	266.863	336.19	1.25978	
59	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Squared	1	219048	129762	1.68808	
59	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	Measured	1	1631.67	2664.55	1.63302	
59	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	Rooted	0	4.28588	6.23127	1.45391	
59	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). [source: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). [source:swissprot;acc:q04446]	Measured	1	4489.19	2765.82	1.6231	
60	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). [source:swissprot;acc:p56377]	Measured	0	47.4756	87.5499	1.8441	
60	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	Ranked	0	11761	15924	1.35397	
60	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	Ranked	1	266.864	336.184	1.25976	
60	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	Squared	0	219.839	59.1928	3.71395	
60	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Squared	1	219048	129762	1.68808	
60	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	Rooted	0	8.48528	12.2882	1.44818	

Legend:
- Rank is the rank after comparing the two networks
- 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/