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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered  : 0
green  : 0.00001
Network Comparison Type  : Divided

Value Type	network_comparison	Interaction Map	red	Rank	description
Measured	1	High confidence	0.00001	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]
	231962		2.31962	7	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]
	1300000		13	6	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	1800000	High confidence	18	65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]
	3500000		35	31	dok-like protein. [refseq;acc:nm_024872]
	3700000	Low confidence	37	22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]
				23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
	6000000	High confidence	60	22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
	8200000		82	20	ero1-like. [refseq;acc:nm_014584]
	15400000		154	95	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
				96	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	28600000	Low confidence	286	44	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]
				45	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	36400000	High confidence	364	1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
		Low confidence
Ranked	1	High confidence	0.00001	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]
				839	cobw-like protein. [refseq;acc:nm_018491]

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.