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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

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Showing element 501 to 550 of 77072 in total

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network_comparison	green	Value Type	Network Comparison Type	red	Interaction Map	Rank	description
0.9646	24.3289	Rooted	Subtracted	23.3643	Low confidence	593	40s ribosomal protein s12. [swissprot;acc:p25398]
0.965708	1.63441	Squared		0.668702	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	Rooted		16.5182		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	Measured	Divided	0.00001	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]
						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.