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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2562 to 2611 of 8289 in total

Network Comparison Type	Divided
Value Type	Ranked
Filtered	1

Rank	Hugo	description	Interaction Map	red	green	network_comparison	
1281	CYP4F3	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	High confidence	218.368	213.22	1.02414	
1282	CTGF	connective tissue growth factor precursor (hypertrophic chondrocyte- specific protein 24). [source:swissprot;acc:p29279]	Low confidence	208.383	203.805	1.02246	
1282	CYP4F8	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	High confidence	218.368	213.22	1.02414	
1283		casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	Low confidence	205.134	200.628	1.02246	
1283	CYP4X1	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	High confidence	218.368	213.22	1.02414	
1284	CYP4F12	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	High confidence	218.368	213.22	1.02414	
1284	FAH	fumarylacetoacetase (ec 3.7.1.2) (fumarylacetoacetate hydrolase) (beta-diketonase) (faa). [source:swissprot;acc:p16930]	Low confidence	202.294	197.852	1.02245	
1285	CYP4F2	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	High confidence	218.368	213.22	1.02414	
1285	PHB	prohibitin. [source:swissprot;acc:p35232]	Low confidence	186.195	182.109	1.02244	
1286	CYP4F11	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	High confidence	218.368	213.22	1.02414	
1286	GNL3	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Low confidence	202.806	198.355	1.02244	
1287	ACSL3	long-chain-fatty-acid--coa ligase 3 (ec 6.2.1.3) (long-chain acyl-coa synthetase 3) (lacs 3). [source:swissprot;acc:o95573]	Low confidence	201.127	196.714	1.02243	
1287	CYP4A22	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [source:sptrembl;acc:q9ntl5]	High confidence	218.368	213.22	1.02414	
1288	C21orf66	gc-rich sequence dna-binding factor homolog. [source:swissprot;acc:q9y5b6]	Low confidence	204.236	199.757	1.02242	
1288	CYP4B1	cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [source:swissprot;acc:p13584]	High confidence	218.368	213.22	1.02414	
1289	FLOT1	flotillin-1. [source:swissprot;acc:o75955]	High confidence	218.368	213.22	1.02414	
1289	GLI2	zinc finger protein gli2 (tax helper protein). [source:swissprot;acc:p10070]	Low confidence	203.073	198.619	1.02242	
1290	PPP1R12B	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [source:refseq;acc:nm_002481]	Low confidence	195.789	191.498	1.02241	
1290	SESN1	sestrin 1 (p53-regulated protein pa26). [source:swissprot;acc:q9y6p5]	High confidence	218.368	213.22	1.02414	
1291	ACSL4	long-chain-fatty-acid--coa ligase 4 (ec 6.2.1.3) (long-chain acyl-coa synthetase 4) (lacs 4). [source:swissprot;acc:o60488]	Low confidence	201.117	196.709	1.02241	
1291	HAS2	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819]	High confidence	221.093	226.399	1.024	
1292	CASP7	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210]	High confidence	233.942	228.46	1.024	
1292	NONO	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	Low confidence	200.544	196.152	1.02239	
1293	CASP3	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [source:swissprot;acc:p42574]	High confidence	233.942	228.46	1.024	
1293	PSPC1	paraspeckle protein 1. [source:refseq;acc:nm_018282]	Low confidence	200.543	196.152	1.02239	
1294	HAS1	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839]	High confidence	221.093	226.399	1.024	
1294	SEC31A	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Low confidence	204.144	199.676	1.02238	
1295	HAS3	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219]	High confidence	221.093	226.399	1.024	
1295	SLC3A1	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	Low confidence	199.695	195.323	1.02238	
1296	SEC31B	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Low confidence	204.174	199.705	1.02238	
1296	SLC37A1	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	High confidence	209.062	204.174	1.02394	
1297	MAPK11	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]	Low confidence	200.193	195.812	1.02237	
1297	PRODH	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	High confidence	209.062	204.174	1.02394	
1298	DLAT	dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [source:swissprot;acc:p10515]	High confidence	206.482	211.404	1.02384	
1298	GLI1	zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [source:swissprot;acc:p08151]	Low confidence	203.074	198.63	1.02237	
1299	ACO2	aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [source:swissprot;acc:q99798]	Low confidence	200.342	195.959	1.02237	
1299	PMPCB	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	High confidence	217.635	212.575	1.0238	
1300		proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Low confidence	199.276	194.918	1.02236	
1300	PMPCA	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	High confidence	217.634	212.576	1.02379	
1301	HCK	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Low confidence	199.276	194.918	1.02236	
1301	TPD52L2	tumor protein d54 (hd54) (d52-like 2). [source:swissprot;acc:o43399]	High confidence	206.852	211.757	1.02371	
1302	FYN	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Low confidence	199.276	194.918	1.02236	
1302	UQCRC1	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	High confidence	217.624	212.584	1.02371	
1303	FGR	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Low confidence	199.276	194.918	1.02236	
1303	FHL5	activator of camp-responsive element modulator (crem) in testis; lim protein act. [source:refseq;acc:nm_020482]	High confidence	269.157	275.531	1.02368	
1304	ABL2	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Low confidence	199.275	194.918	1.02235	
1304	GSR	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	High confidence	207.387	212.275	1.02357	
1305	GPAM	glycerol-3-phosphate acyltransferase, mitochondrial precursor (ec 2.3.1.15) (gpat). [source:swissprot;acc:q9hcl2]	Low confidence	204.064	199.602	1.02235	
1305	PPP3CA	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	High confidence	218.439	213.436	1.02344	
1306	ABL1	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Low confidence	199.275	194.918	1.02235	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/