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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered  : 0
green  : 0.00001
Network Comparison Type  : Divided

Value Type	Rank	network_comparison	Interaction Map	description	red
Measured	1	36400000	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364
			Low confidence
	6	1300000		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13
	7	231962		tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962
	20	8200000	High confidence	ero1-like. [refseq;acc:nm_014584]	82
	22	3700000	Low confidence	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	37
		6000000	High confidence	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60
	23	3700000	Low confidence	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	37
	31	3500000	High confidence	dok-like protein. [refseq;acc:nm_024872]	35
	44	28600000	Low confidence	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	286
	45			neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	65	1800000	High confidence	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	18
	95	15400000		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	154
	96			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	494	1		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0.00001
	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]
	837		Low confidence	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	501		High confidence	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]
	837		Low confidence	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	2	561325	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325
	3			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	5	32402.4	Low confidence	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0.324024
	6			carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
	8	159148	High confidence	ero1-like. [refseq;acc:nm_014584]	1.59148
	9	4000	Low confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.04
		85207.1	High confidence	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0.852071
	13	219.609	Low confidence	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0.00219609
		28994.1	High confidence	dok-like protein. [refseq;acc:nm_024872]	0.289941
	17	7668.64		rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	0.0766864
	68	3136000		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	31.36
	73		Low confidence

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.