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 1218 to 1267 of 3228 in total

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

Rank	description	red	green	network_comparison	
1218	cyclin m4; ancient conserved domain protein 4. [source:refseq;acc:nm_020184]	5736	6226.52	1.08552	
1219	tcd37 homolog; prune. [source:refseq;acc:nm_021222]	5735.95	6226.46	1.08552	
1220	cyclin m3; ancient conserved domain protein 3. [source:refseq;acc:nm_017623]	5735.65	6226.13	1.08551	
1221	cyclin m2; ancient conserved domain protein 2. [source:refseq;acc:nm_017649]	5736.34	6226.88	1.08551	
1222	cyclin m1; ancient conserved domain protein 1. [source:refseq;acc:nm_020348]	5735.74	6226.23	1.08551	
1223	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	6011.44	6524.55	1.08536	
1224	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	4331.35	4700.91	1.08532	
1225	apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	5546.5	6019.57	1.08529	
1226	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	5997.24	6508.62	1.08527	
1227	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	5973.95	6483.32	1.08527	
1228	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	5998.58	6509.65	1.0852	
1229	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	5998.69	6509.74	1.08519	
1230	dystrobrevin binding protein 1; dysbindin. [source:refseq;acc:nm_032122]	5678.02	6161.65	1.08518	
1231	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	5132.68	5569.54	1.08511	
1232	nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	5869.24	6367.8	1.08494	
1233	tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [source:swissprot;acc:p14679]	6004.54	6514.24	1.08489	
1234	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	5807.83	6300.47	1.08482	
1235	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	5807.83	6300.47	1.08482	
1236	p10-binding protein. [source:refseq;acc:nm_024491]	5594.18	6067.49	1.08461	
1237	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [source:swissprot;acc:q9y3q8]	5873.56	6370.31	1.08457	
1238	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	5873.56	6370.31	1.08457	
1239	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	5654.53	6132.76	1.08457	
1240	retinoic acid induced 17; pias-like protein hzimp10. [source:refseq;acc:nm_020338]	5654.54	6132.69	1.08456	
1241	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	6436.19	6980.13	1.08451	
1242	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	11143.5	10276.3	1.08439	
1243	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	11143.5	10276.3	1.08439	
1244	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [source:refseq;acc:nm_016538]	4835.55	5243.23	1.08431	
1245	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	4835.55	5243.23	1.08431	
1246	p53-related protein kinase (ec 2.7.1.-) (nori-2). [source:swissprot;acc:q96s44]	5346.11	5796.72	1.08429	
1247	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	6278.76	6807.51	1.08421	
1248	protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [source:swissprot;acc:p17706]	6275.86	6803.95	1.08415	
1249	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	4413.55	4784.6	1.08407	
1250	huntingtin interacting protein 1 (hip-i). [source:swissprot;acc:o00291]	10733.4	9902.6	1.0839	
1251	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	8618.32	9340.98	1.08385	
1252	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	8618.32	9340.98	1.08385	
1253	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	8618.32	9340.98	1.08385	
1254	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	10725.6	9896.32	1.0838	
1255	serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [source:swissprot;acc:p33172]	5438.66	5893.87	1.0837	
1256	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	10719	9891.08	1.0837	
1257	immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [source:swissprot;acc:p78318]	5438.66	5893.87	1.0837	
1258	glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	6251.32	6774.12	1.08363	
1259	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [source:refseq;acc:nm_139204]	5685.38	6157.7	1.08308	
1260	rad54-like protein; rad54 homolog. [source:refseq;acc:nm_003579]	5754.84	6232.83	1.08306	
1261	epidermal growth factor receptor kinase substrate eps8. [source:swissprot;acc:q12929]	5685.34	6157.53	1.08305	
1262	serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	5894.47	6383.73	1.083	
1263	gtp binding protein 2. [source:refseq;acc:nm_019096]	5894.47	6383.73	1.083	
1264	cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [source:swissprot;acc:q99941]	5894.47	6383.73	1.083	
1265	dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [source:refseq;acc:nm_012135]	5894.47	6383.73	1.083	
1266	sfrs protein kinase 2 isoform b. [source:refseq;acc:nm_182691]	5894.47	6383.73	1.083	
1267	cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [source:swissprot;acc:p18850]	5894.47	6383.73	1.083	

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/