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 2058 to 2107 of 3228 in total

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

Rank	description	red	green	network_comparison	
2058	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [source:swissprot;acc:q9ujc5]	218.79	216.981	1.00834	
2059	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [source:refseq;acc:nm_181782]	218.79	216.981	1.00834	
2060	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [source:sptrembl;acc:q9h125]	218.79	216.981	1.00834	
2061	tbc1 domain family protein c22orf4-like (fragment). [source:swissprot;acc:q9nu19]	218.79	216.981	1.00834	
2062	tbc1 domain family protein c22orf4. [source:swissprot;acc:q8wua7]	218.79	216.981	1.00834	
2063	ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	207.638	205.923	1.00833	
2064	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [source:refseq;acc:nm_005763]	207.655	205.939	1.00833	
2065	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [source:swissprot;acc:q16781]	214.328	212.561	1.00831	
2066	proliferating cell nuclear antigen (pcna) (cyclin). [source:swissprot;acc:p12004]	229.102	231.001	1.00829	
2067	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [source:swissprot;acc:p30566]	193.226	191.639	1.00828	
2068	fas apoptotic inhibitory molecule. [source:refseq;acc:nm_018147]	220.8	222.61	1.0082	
2069	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [source:swissprot;acc:q02750]	217.555	215.807	1.0081	
2070	rac gtpase activating protein 1; gtpase activating protein. [source:refseq;acc:nm_013277]	223.199	225.008	1.0081	
2071	similar to kinase suppressor of ras (fragment). [source:sptrembl;acc:q8ivt5]	217.555	215.807	1.0081	
2072	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [source:swissprot;acc:p36507]	217.555	215.807	1.0081	
2073	topoisomerase-related function protein 4-2. [source:refseq;acc:nm_022447]	229.267	227.433	1.00806	
2074	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [source:swissprot;acc:p54098]	216.324	214.599	1.00804	
2075	cd109; gov system alloantigens on platelets. [source:refseq;acc:nm_133493]	221.703	223.483	1.00803	
2076	peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [source:swissprot;acc:q13526]	221.703	223.483	1.00803	
2077	iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [source:swissprot;acc:p78413]	221.703	223.483	1.00803	
2078	fidgetin-like 1. [source:refseq;acc:nm_022116]	215.511	213.814	1.00794	
2079	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [source:swissprot;acc:o75747]	215.967	214.28	1.00787	
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	214.28	1.00787	
2081	dynamin 1-like protein isoform 3; dynamin-like protein. [source:refseq;acc:nm_005690]	215.967	214.28	1.00787	
2082	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [source:refseq;acc:nm_002645]	215.967	214.28	1.00787	
2083	vacuolar protein sorting 16 (hvps16). [source:swissprot;acc:q9h269]	215.258	213.579	1.00786	
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	224.293	1.00784	
2085	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p50213]	222.58	224.32	1.00782	
2086	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:o43837]	222.58	224.32	1.00782	
2087	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [source:swissprot;acc:p51553]	222.58	224.32	1.00782	
2088	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	218.124	216.433	1.00781	
2089	serologically defined colon cancer antigen 16. [source:refseq;acc:nm_006649]	215.144	213.479	1.0078	
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	224.344	1.00779	
2091	rna, u transporter 1; snurportin-1. [source:refseq;acc:nm_005701]	211.679	210.052	1.00775	
2092	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [source:refseq;acc:nm_016581]	211.992	210.369	1.00772	
2093	ribokinase (ec 2.7.1.15). [source:swissprot;acc:q9h477]	209.994	208.387	1.00771	
2094	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	207.321	205.747	1.00765	
2095	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	229.266	227.53	1.00763	
2096	limkain beta 2. [source:refseq;acc:nm_025140]	217.723	216.089	1.00756	
2097	delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	214.979	213.39	1.00745	
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	178.831	1.00741	
2099	ubiquitin-like protein smt3a. [source:swissprot;acc:p55854]	211.71	213.27	1.00737	
2100	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	211.71	213.27	1.00737	
2101	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	211.71	213.27	1.00737	
2102	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [source:swissprot;acc:p10159]	208.727	210.263	1.00736	
2103	transketolase (ec 2.2.1.1) (tk). [source:swissprot;acc:p29401]	214.666	216.236	1.00731	
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [source:swissprot;acc:p23919]	209.328	207.813	1.00729	
2105	eif-5a2 protein. [source:refseq;acc:nm_020390]	208.591	210.111	1.00729	
2106	insulin gene enhancer protein isl-1 (islet-1). [source:swissprot;acc:p20663]	197.489	196.061	1.00728	
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	217.801	1.00727	

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/