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

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Showing element 930 to 979 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
117	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Rooted	Subtracted	40.5691	25.4263	15.1428	
117	high-mobility group 20a. [source:refseq;acc:nm_018200]	Ranked	Subtracted	208.588	171.778	36.81	
117	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Measured	Subtracted	9276.47	7090.37	2186.1	
117	neuralized-like. [source:refseq;acc:nm_004210]	Ranked	Divided	332.326	266.948	1.24491	
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Measured	Divided	21185	28492	1.34491	
117	transcription factor jun-b. [source:swissprot;acc:p17275]	Rooted	Divided	63.4173	79.5311	1.25409	
117	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Squared	Subtracted	81888.8	56306.5	25582.3	
118	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Measured	Subtracted	9275.1	7089.65	2185.45	
118	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Rooted	Divided	50.3065	62.9788	1.2519	
118	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]	Ranked	Divided	284.753	228.934	1.24382	
118	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	Subtracted	37.2205	52.2064	14.9859	
118	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Ranked	Subtracted	274.027	237.79	36.237	
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Measured	Divided	21185	28492	1.34491	
118	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Squared	Divided	210445	136779	1.53858	
118	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Squared	Subtracted	81888.8	56306.5	25582.3	
119	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Measured	Subtracted	12998.5	15138.2	2139.7	
119	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Ranked	Subtracted	281.582	246.371	35.211	
119	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Squared	Subtracted	81606.8	56215.8	25391	
119	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Squared	Divided	210335	136716	1.53848	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	Divided	21185	28492	1.34491	
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Ranked	Divided	318.982	259.004	1.23157	
119	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Rooted	Subtracted	63.6507	48.7127	14.938	
119	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	Divided	50.3247	62.9892	1.25166	
120	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Squared	Subtracted	81592.1	56211.1	25381	
120	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Rooted	Subtracted	40.081	25.1546	14.9264	
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	Divided	5136.78	6895.98	1.34247	
120	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	Divided	50.3333	62.9942	1.25154	
120	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Ranked	Subtracted	227.199	192.715	34.484	
120	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Squared	Divided	210199	136638	1.53836	
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	Divided	269.278	327.709	1.21699	
120	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Measured	Subtracted	4932.27	7033.29	2101.02	
121	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Squared	Subtracted	81527.6	56190.6	25337	
121	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Ranked	Divided	269.254	327.655	1.2169	
121	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Rooted	Divided	50.339	62.9975	1.25147	
121	jun dimerization protein. [source:refseq;acc:nm_130469]	Measured	Subtracted	4932.27	7033.29	2101.02	
121	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Ranked	Subtracted	227.202	192.823	34.379	
121	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Rooted	Subtracted	63.6205	48.8838	14.7367	
121	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Squared	Divided	199594	130021	1.53509	
121	transcription factor jun-b. [source:swissprot;acc:p17275]	Measured	Divided	5579.18	7488.4	1.3422	
122	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Squared	Divided	201896	131906	1.53061	
122	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Ranked	Subtracted	199.949	234.187	34.238	
122	fos-related antigen 2. [source:swissprot;acc:p15408]	Measured	Subtracted	4941.95	7037.11	2095.16	
122	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Squared	Subtracted	81520.8	56188.5	25332.3	
122	high-mobility group 20a. [source:refseq;acc:nm_018200]	Measured	Divided	5140.14	6893.53	1.34112	
122	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Rooted	Subtracted	60.9342	75.1387	14.2045	
122	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]	Ranked	Divided	269.248	327.642	1.21688	
122	transcription factor jun-d. [source:swissprot;acc:p17535]	Rooted	Divided	63.636	79.6225	1.25122	
123	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	Squared	Subtracted	81478.9	56175.2	25303.7	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Measured	Divided	24260.3	18172.1	1.33503	
123	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Rooted	Subtracted	46.7419	60.9337	14.1918	

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/