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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

green	network_comparison	Rank	description	Interaction Map	red	Network Comparison Type
0	0	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]	High confidence	0	Subtracted
		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	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	Low confidence
		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]
	2.31962	822	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		2.31962
	13	777	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		13
	18	429	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	High confidence	18
	35	386	dok-like protein. [refseq;acc:nm_024872]		35
	37	648	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Low confidence	37
		649	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
	60	338	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence	60
	82	316	ero1-like. [refseq;acc:nm_014584]		82
	154	206	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154
		207	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	286	200	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	286
		201	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	364	88	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	364
		170		Low confidence
0.00001	1	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]	High confidence	0.00001	Divided
		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	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	Low confidence
		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	7	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		2.31962
	1300000	6	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		13
	1800000	65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	High confidence	18
	3500000	31	dok-like protein. [refseq;acc:nm_024872]		35

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.