MK5 Microarray Data

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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Gene	Value Type	Network Comparison Type	Rank	description	Interaction Map	green	network_comparison	red	Filtered

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Showing element 2063 to 2112 of 3228 in total

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

Rank	description	green	network_comparison	red
2063	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	205.923	1.00833	207.638
2064	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	205.939		207.655
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). [swissprot;acc:q16781]	212.561	1.00831	214.328
2066	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	231.001	1.00829	229.102
2067	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	191.639	1.00828	193.226
2068	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	222.61	1.0082	220.8
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). [swissprot;acc:q02750]	215.807	1.0081	217.555
2070	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	225.008		223.199
2071	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	215.807		217.555
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). [swissprot;acc:p36507]
2073	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	227.433	1.00806	229.267
2074	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	214.599	1.00804	216.324
2075	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	223.483	1.00803	221.703
2076	peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
2077	iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
2078	fidgetin-like 1. [refseq;acc:nm_022116]	213.814	1.00794	215.511
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). [swissprot;acc:o75747]	214.28	1.00787	215.967
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). [swissprot;acc:o00750]
2081	dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
2082	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]
2083	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	213.579	1.00786	215.258
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). [swissprot;acc:q06210]	224.293	1.00784	222.548
2085	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213]	224.32	1.00782	222.58
2086	isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837]
2087	isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553]
2088	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	216.433	1.00781	218.124
2089	serologically defined colon cancer antigen 16. [refseq;acc:nm_006649]	213.479	1.0078	215.144
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). [swissprot;acc:o94808]	224.344	1.00779	222.609
2091	rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701]	210.052	1.00775	211.679
2092	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	210.369	1.00772	211.992
2093	ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477]	208.387	1.00771	209.994
2094	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	205.747	1.00765	207.321
2095	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	227.53	1.00763	229.266
2096	limkain beta 2. [refseq;acc:nm_025140]	216.089	1.00756	217.723
2097	delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834]	213.39	1.00745	214.979
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). [swissprot;acc:o60858]	178.831	1.00741	177.515
2099	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	213.27	1.00737	211.71
2100	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]
2101	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]
2102	eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159]	210.263	1.00736	208.727
2103	transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401]	216.236	1.00731	214.666
2104	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	207.813	1.00729	209.328
2105	eif-5a2 protein. [refseq;acc:nm_020390]	210.111		208.591
2106	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	196.061	1.00728	197.489
2107	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]	217.801	1.00727	216.23
2108	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	217.93	1.00726	216.36
2109	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	217.47	1.00718	219.032
2110	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	209.607	1.00712	211.099
2111	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	217.511	1.00706	219.047
2112	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	224.989	1.00705	223.415

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.