Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

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Showing element 1 to 50 of 38536 in total

Filtered

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Network Comparison Type

: Divided

Value Type	network_comparison	Rank	Interaction Map	description	red
Measured	1	494	High confidence	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]
	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	High confidence	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	18
	3500000	31	High confidence	dok-like protein. [refseq;acc:nm_024872]	35
	3700000	22	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
	3700000	23	Low confidence	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	37
	6000000	22	High confidence	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60
	8200000	20		ero1-like. [refseq;acc:nm_014584]	82
	15400000	95		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	154
	15400000	96		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	154
	28600000	44	Low confidence	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	286
	28600000	45	Low confidence	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	286
	36400000	1	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364
	36400000	1	Low confidence		364
Ranked	1	501	High confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001
		502	High confidence	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		494	High confidence	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]
		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]

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.

- http://analysis.yellowcouch.org/