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 Network Comparison Type Value Type Interaction Map red Filtered network_comparison green

Results: HTML CSV LaTeX

Showing element 2080 to 2129 of 3228 in total

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

Rank	description	red	network_comparison	green	
2080	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	215.967	1.00787	214.28	
2081	dynamin 1-like protein isoform 3; dynamin-like protein. [source:refseq;acc:nm_005690]	215.967	1.00787	214.28	
2082	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [source:refseq;acc:nm_002645]	215.967	1.00787	214.28	
2083	vacuolar protein sorting 16 (hvps16). [source:swissprot;acc:q9h269]	215.258	1.00786	213.579	
2084	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	222.548	1.00784	224.293	
2085	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p50213]	222.58	1.00782	224.32	
2086	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:o43837]	222.58	1.00782	224.32	
2087	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p51553]	222.58	1.00782	224.32	
2088	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	218.124	1.00781	216.433	
2089	serologically defined colon cancer antigen 16. [source:refseq;acc:nm_006649]	215.144	1.0078	213.479	
2090	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [source:swissprot;acc:o94808]	222.609	1.00779	224.344	
2091	rna, u transporter 1; snurportin-1. [source:refseq;acc:nm_005701]	211.679	1.00775	210.052	
2092	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [source:refseq;acc:nm_016581]	211.992	1.00772	210.369	
2093	ribokinase (ec 2.7.1.15). [source:swissprot;acc:q9h477]	209.994	1.00771	208.387	
2094	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	207.321	1.00765	205.747	
2095	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	229.266	1.00763	227.53	
2096	limkain beta 2. [source:refseq;acc:nm_025140]	217.723	1.00756	216.089	
2097	delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	214.979	1.00745	213.39	
2098	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	177.515	1.00741	178.831	
2099	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	211.71	1.00737	213.27	
2100	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	211.71	1.00737	213.27	
2101	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	211.71	1.00737	213.27	
2102	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	208.727	1.00736	210.263	
2103	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	214.666	1.00731	216.236	
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	209.328	1.00729	207.813	
2105	eif-5a2 protein. [source:refseq;acc:nm_020390]	208.591	1.00729	210.111	
2106	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	197.489	1.00728	196.061	
2107	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [source:refseq;acc:nm_005358]	216.23	1.00727	217.801	
2108	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	216.36	1.00726	217.93	
2109	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [source:swissprot;acc:p49792]	219.032	1.00718	217.47	
2110	conserved oligomeric golgi complex component 6. [source:swissprot;acc:q9y2v7]	211.099	1.00712	209.607	
2111	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	219.047	1.00706	217.511	
2112	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [source:swissprot;acc:q9y2y1]	223.415	1.00705	224.989	
2113	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	219.055	1.007	217.533	
2114	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [source:swissprot;acc:p07098]	214.632	1.007	213.14	
2115	ba304i5.1 (novel lipase) (fragment). [source:sptrembl;acc:q96lg2]	214.632	1.007	213.14	
2116	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [source:swissprot;acc:p38571]	214.632	1.007	213.14	
2117	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [source:swissprot;acc:q9np81]	214.632	1.007	213.14	
2118	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [source:swissprot;acc:p49591]	214.632	1.007	213.14	
2119	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [source:refseq;acc:nm_020122]	221.248	1.00696	222.788	
2120	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [source:swissprot;acc:q9uhi7]	221.248	1.00696	222.788	
2121	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	221.248	1.00696	222.788	
2122	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	206.473	1.00696	207.911	
2123	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	221.248	1.00696	222.788	
2124	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	221.248	1.00696	222.788	
2125	shc transforming protein. [source:swissprot;acc:p29353]	221.248	1.00696	222.788	
2126	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	221.248	1.00696	222.788	
2127	neuronal shc. [source:refseq;acc:nm_016848]	221.248	1.00696	222.788	
2128	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	221.248	1.00696	222.788	
2129	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	221.248	1.00696	222.788	

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/