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

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network_comparison	green	red	Value Type	Interaction Map	Network Comparison Type	Rank	description
0.9646	24.3289	23.3643	Rooted	Low confidence	Subtracted	593	40s ribosomal protein s12. [swissprot;acc:p25398]
0.965708	1.63441	0.668702	Squared	High confidence		447	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
0.9672	17.4854	16.5182	Rooted			381	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]
0.9753	43.0082	42.0329				379	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]
						380	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
0.9767	16.5084	15.5317		Low confidence		592	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
0.9771	33.4964	34.4735				591	neprilysin (ec 3.4.24.11) (neutral endopeptidase) (nep) (enkephalinase) (common acute lymphocytic leukemia antigen) (calla) (neutral endopeptidase 24.11) (cd10). [swissprot;acc:p08473]
0.9803	19.119	18.1387				590	ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03]
0.9827	25.6434	24.6607				589	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
0.9843	19.2328	20.2171				588	kappa b-ras 1. [refseq;acc:nm_020345]
0.9856	33.9829	34.9685				587	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]
0.9892	26.8952	25.906				586	60s ribosomal protein l9. [swissprot;acc:p32969]
0.98968	6.55744	5.56776		High confidence		378	methyltransferase like 2. [refseq;acc:nm_018396]
0.9907	29.8694	30.8601				377	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
0.995	26.0677	27.0627		Low confidence		585	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]
1	0.00001	0.00001	Measured	High confidence	Divided	494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
						495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
						496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
						497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
						498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
						500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
						501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
						502	brca1 associated protein. [refseq;acc:nm_006768]
				Low confidence		837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
						838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
						839	cobw-like protein. [refseq;acc:nm_018491]
						840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
						842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
						843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
			Ranked	High confidence		501	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
						502	brca1 associated protein. [refseq;acc:nm_006768]
				Low confidence		837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
						838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
						839	cobw-like protein. [refseq;acc:nm_018491]
						841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
						842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
						843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
			Squared	High confidence		494	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
						495	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
						496	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
						497	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
						498	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
						499	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
						500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
						501	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
						502	brca1 associated protein. [refseq;acc:nm_006768]
				Low confidence		837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
						838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]

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.