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 2500 to 2549 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2500	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	3804.53	3705.05	1.02685	
2501	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	6562.71	6738.23	1.02675	
2502	glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p00367]	6562.71	6738.23	1.02675	
2503	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [source:swissprot;acc:p53597]	5996.06	6155.81	1.02664	
2504	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [source:swissprot;acc:q9p2r7]	5996.06	6155.81	1.02664	
2505	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	6237.83	6400.74	1.02612	
2506	2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	6200.39	6362.25	1.0261	
2507	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	4243.44	4352.56	1.02571	
2508	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	6469.44	6634.31	1.02548	
2509	reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [source:swissprot;acc:o95197]	6202.78	6360.79	1.02547	
2510	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [source:swissprot;acc:q99643]	6256.49	6415.21	1.02537	
2511	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	6256.42	6415.04	1.02535	
2512	reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [source:swissprot;acc:o75298]	6203.05	6360.18	1.02533	
2513	reticulon 1 (neuroendocrine-specific protein). [source:swissprot;acc:q16799]	6204.25	6360.69	1.02521	
2514	eh-domain containing protein 1 (testilin) (hpast1). [source:swissprot;acc:q9h4m9]	6203.92	6360.25	1.0252	
2515	eh-domain containing protein 3. [source:swissprot;acc:q9nzn3]	6203.94	6360.25	1.0252	
2516	eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [source:swissprot;acc:q9h223]	6203.95	6360.24	1.02519	
2517	eh-domain containing protein 2. [source:swissprot;acc:q9nzn4]	6203.96	6360.24	1.02519	
2518	sin3 associated polypeptide p18 (2hor0202). [source:swissprot;acc:o00422]	6204.15	6360.27	1.02516	
2519	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	5964.17	6113.96	1.02511	
2520	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	5964.17	6113.96	1.02511	
2521	17 beta-hydroxysteroid dehydrogenase. [source:sptrembl;acc:q13034]	5964.17	6113.96	1.02511	
2522	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [source:refseq;acc:nm_015725]	5964.17	6113.96	1.02511	
2523	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	3803.04	3710.01	1.02508	
2524	myo-inositol 1-phosphate synthase a1. [source:refseq;acc:nm_016368]	8695.15	8912.98	1.02505	
2525	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	8695.15	8912.98	1.02505	
2526	ubiquitin-like protein gdx (ubiquitin-like protein 4). [source:swissprot;acc:p11441]	8695.15	8912.98	1.02505	
2527	large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [source:swissprot;acc:p46379]	8695.15	8912.98	1.02505	
2528	reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [source:swissprot;acc:q9nqc3]	6205.14	6359.44	1.02487	
2529	protein cgi-147. [source:swissprot;acc:q9y3e5]	6436.43	6283	1.02442	
2530	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	3880.5	3788.42	1.02431	
2531	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [source:swissprot;acc:q01780]	6141.97	6291.08	1.02428	
2532	60s ribosomal protein l15. [source:swissprot;acc:p39030]	4888.72	5006.1	1.02401	
2533	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	3847.84	3759.28	1.02356	
2534	thyroid receptor interacting protein 12 (trip12). [source:swissprot;acc:q14669]	6452.33	6603.94	1.0235	
2535	dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	6452.33	6603.94	1.0235	
2536	sorting nexin 1. [source:swissprot;acc:q13596]	5932.05	6071.35	1.02348	
2537	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [source:swissprot;acc:p29803]	6669.22	6824.41	1.02327	
2538	estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [source:swissprot;acc:p51659]	7121.07	7286.61	1.02325	
2539	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	3805.17	3718.86	1.02321	
2540	pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [source:swissprot;acc:p08559]	6672.69	6827.51	1.0232	
2541	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	8542.13	8740.23	1.02319	
2542	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	4708.98	4817.39	1.02302	
2543	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	8565.3	8760.3	1.02277	
2544	peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [source:swissprot;acc:p30044]	6239.69	6378.35	1.02222	
2545	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	8285.65	8107.49	1.02197	
2546	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [source:swissprot;acc:p36954]	4763.99	4868.66	1.02197	
2547	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [source:swissprot;acc:o15530]	3370.46	3444.18	1.02187	
2548	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	4725.79	4824.4	1.02087	
2549	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	4725.79	4824.4	1.02087	

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/