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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1051 to 1100 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
526	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Divided	10639.9	12117.4	1.13886	
526	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	Subtracted	5207.78	6010.45	802.67	
527	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [source:swissprot;acc:o75688]	Divided	4775.11	5438.18	1.13886	
527	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	Subtracted	4700.42	5492.63	792.21	
528	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	Divided	10635.3	12111.4	1.13879	
528	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	Subtracted	5244.71	6036.27	791.56	
529	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Divided	8600.02	9792.49	1.13866	
529	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	Subtracted	5244.88	6036.38	791.5	
530	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Divided	8600.02	9792.49	1.13866	
530	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	Subtracted	5246.38	6037.37	790.99	
531	prohibitin. [source:swissprot;acc:p35232]	Subtracted	5773.45	6563.69	790.24	
531	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [source:swissprot;acc:q00403]	Divided	4651.88	5296.78	1.13863	
532	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Subtracted	5773.45	6563.69	790.24	
532	thyroid receptor interacting protein 3 (trip-3) (fragment). [source:swissprot;acc:q15649]	Divided	4651.88	5296.78	1.13863	
533	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [source:swissprot;acc:p07099]	Subtracted	11785.4	10995.3	790.1	
533	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	Divided	4651.88	5296.78	1.13863	
534	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	Divided	4651.88	5296.78	1.13863	
534	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	Subtracted	5233.86	6022.6	788.74	
535	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	Divided	10603.5	12069.5	1.13826	
535	vinculin (metavinculin). [source:swissprot;acc:p18206]	Subtracted	5958.23	6743.37	785.14	
536	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Divided	10603.5	12069.5	1.13826	
536	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	Subtracted	6227.87	7012.9	785.03	
537	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	Subtracted	6228.39	7013.19	784.8	
537	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Divided	10603.5	12069.5	1.13826	
538	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Subtracted	6228.39	7013.19	784.8	
538	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Divided	10603.5	12069.4	1.13825	
539	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	Subtracted	6228.39	7013.19	784.8	
539	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	Divided	10603.5	12069.4	1.13825	
540	gk001 protein. [source:refseq;acc:nm_020198]	Divided	10603.5	12069.4	1.13825	
540	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Subtracted	6228.39	7013.19	784.8	
541	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	Divided	10600.3	12065.2	1.13819	
541	limkain b1. [source:refseq;acc:nm_019081]	Subtracted	6228.39	7013.19	784.8	
542	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Subtracted	6228.39	7013.19	784.8	
542	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [source:swissprot;acc:p31749]	Divided	3889.27	4426.74	1.13819	
543	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	Divided	10599.9	12064.7	1.13819	
543	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Subtracted	6228.39	7013.19	784.8	
544	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Subtracted	6228.39	7013.19	784.8	
544	rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [source:swissprot;acc:q9y243]	Divided	3889.27	4426.74	1.13819	
545	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Subtracted	6228.39	7013.19	784.8	
545	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [source:swissprot;acc:p31751]	Divided	3889.27	4426.74	1.13819	
546	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Subtracted	6228.39	7013.19	784.8	
546	zinc finger protein t86. [source:swissprot;acc:o00488]	Divided	4052.77	4612.54	1.13812	
547	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Subtracted	6228.39	7013.19	784.8	
547	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Divided	5291.92	6020.19	1.13762	
548	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Divided	8268.19	9405.85	1.13759	
548	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Subtracted	6228.39	7013.19	784.8	
549	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Divided	5865.79	6671.23	1.13731	
549	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Subtracted	6228.42	7013.21	784.79	
550	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Subtracted	6228.97	7013.53	784.56	
550	prohibitin. [source:swissprot;acc:p35232]	Divided	5773.45	6563.69	1.13687	

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/