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 1025 to 1074 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
513	1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [source:swissprot;acc:q9nrz7]	Divided	7485.08	8543.66	1.14143	
513	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Subtracted	6912.09	7734.41	822.32	
514	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	Divided	7477	8532.02	1.1411	
514	di-ras2. [source:refseq;acc:nm_017594]	Subtracted	6912.08	7734.39	822.31	
515	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Divided	3890.53	4439.07	1.14099	
515	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	Subtracted	5084.26	5904.1	819.84	
516	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	1153.5	339.5	814	
516	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	Divided	4910.6	5600.61	1.14051	
517	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	Divided	4910.6	5600.61	1.14051	
517	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	1153.5	339.5	814	
518	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Subtracted	1153.5	339.5	814	
518	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	Divided	4910.6	5600.61	1.14051	
519	db83 protein. [source:swissprot;acc:p57088]	Subtracted	1153.5	339.5	814	
519	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Divided	9648.27	10994.9	1.13957	
520	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Divided	9642.22	10986.4	1.13941	
520	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Subtracted	3858.52	4669.27	810.75	
521	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	Subtracted	6143.52	6950.75	807.23	
521	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	Divided	5390.78	6142.07	1.13937	
522	calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [source:swissprot;acc:p98194]	Subtracted	6148.94	6955.76	806.82	
522	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Divided	9634.98	10976.2	1.1392	
523	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	Divided	10640.2	12117.8	1.13887	
523	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]	Subtracted	5865.79	6671.23	805.44	
524	aquaporin 5. [source:swissprot;acc:p55064]	Divided	10640	12117.6	1.13887	
524	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Subtracted	5206.9	6010.04	803.14	
525	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Divided	10639.8	12117.3	1.13887	
525	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	Subtracted	5207.03	6010.1	803.07	
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	

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/