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 2477 to 2526 of 3228 in total

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

Rank	description	red	green	network_comparison	
2477	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	3568.84	3676.43	1.03015	
2478	zinc finger protein 232. [source:swissprot;acc:q9uny5]	3568.96	3676.57	1.03015	
2479	zinc finger protein 99. [source:refseq;acc:nm_032164]	3568.99	3676.6	1.03015	
2480	zinc finger protein 305. [source:swissprot;acc:o43309]	3568.95	3676.56	1.03015	
2481	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	3568.8	3676.39	1.03015	
2482	zinc finger protein 213 (putative transcription factor cr53). [source:swissprot;acc:o14771]	3568.99	3676.61	1.03015	
2483	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	3568.8	3676.38	1.03014	
2484	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	3568.45	3675.97	1.03013	
2485	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	3568.18	3675.65	1.03012	
2486	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	3626.38	3734.8	1.0299	
2487	tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [source:swissprot;acc:p18074]	6963.12	7170.02	1.02971	
2488	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	5637.59	5804.47	1.0296	
2489	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	5637.59	5804.47	1.0296	
2490	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	6294.37	6472.9	1.02836	
2491	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	3436.65	3531.96	1.02773	
2492	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	3436.65	3531.96	1.02773	
2493	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	3436.65	3531.96	1.02773	
2494	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	3436.65	3531.96	1.02773	
2495	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	3436.65	3531.96	1.02773	
2496	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	5534.46	5684.97	1.0272	
2497	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	7002.3	7192.25	1.02713	
2498	helicase (fragment). [source:sptrembl;acc:q92771]	7002.03	7191.88	1.02711	
2499	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	8186.02	7971.27	1.02694	
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	

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/