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

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

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Showing element 1 to 50 of 77072 in total

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Filtered  : 0
network_comparison  : 0
Network Comparison Type  : Subtracted
red  : 0

Value Type	Interaction Map	Rank	description
Measured	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]
		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]
Rooted	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]

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.