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

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Showing element 2051 to 2100 of 3228 in total

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

Rank	description	green	red	network_comparison
2051	oxidation resistance 1. [refseq;acc:nm_181354]	216.981	218.79	1.00834
2052	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	205.95	207.667
2053	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	216.981	218.79
2054	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	205.948	207.665
2055	dymeclin. [refseq;acc:nm_017653]	216.981	218.79
2056	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
2057	lats homolog 1. [refseq;acc:nm_004690]
2058	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
2059	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
2060	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
2061	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
2062	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
2063	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	205.923	207.638	1.00833
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	214.328	1.00831
2066	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	231.001	229.102	1.00829
2067	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	191.639	193.226	1.00828
2068	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	222.61	220.8	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). [swissprot;acc:q02750]	215.807	217.555	1.0081
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	229.267	1.00806
2074	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	214.599	216.324	1.00804
2075	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	223.483	221.703	1.00803
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	215.511	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). [swissprot;acc:o75747]	214.28	215.967	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). [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	215.258	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). [swissprot;acc:q06210]	224.293	222.548	1.00784
2085	isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213]	224.32	222.58	1.00782
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	218.124	1.00781
2089	serologically defined colon cancer antigen 16. [refseq;acc:nm_006649]	213.479	215.144	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). [swissprot;acc:o94808]	224.344	222.609	1.00779
2091	rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701]	210.052	211.679	1.00775
2092	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	210.369	211.992	1.00772
2093	ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477]	208.387	209.994	1.00771
2094	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	205.747	207.321	1.00765
2095	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	227.53	229.266	1.00763
2096	limkain beta 2. [refseq;acc:nm_025140]	216.089	217.723	1.00756
2097	delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834]	213.39	214.979	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). [swissprot;acc:o60858]	178.831	177.515	1.00741
2099	ubiquitin-like protein smt3a. [swissprot;acc:p55854]	213.27	211.71	1.00737
2100	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]

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.