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

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Showing element 1 to 50 of 77072 in total

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

Interaction Map	Rank	Value Type	description
High confidence	494	Measured	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
		Squared
		Rooted
	495	Measured	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
		Squared
		Rooted
	496	Measured	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
		Squared
		Rooted
	497	Measured	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
		Squared
		Rooted
	498	Measured	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		Squared
		Rooted
	499	Measured	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		Squared
		Rooted
	500	Measured	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
		Squared
		Rooted
	501	Measured	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
		Ranked	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		Squared	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
		Rooted
	502	Measured	brca1 associated protein. [refseq;acc:nm_006768]
		Ranked
		Squared
		Rooted
Low confidence	837	Measured	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
		Ranked
		Squared
		Rooted
	838	Measured	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
		Ranked
		Squared
		Rooted
	839	Measured	cobw-like protein. [refseq;acc:nm_018491]
		Ranked
		Squared
		Rooted
	840	Measured	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		Squared
		Rooted
	841	Measured	gamma-glutamyltransferase. [sptrembl;acc:q14390]
		Ranked
		Squared
		Rooted
	842	Measured	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
		Ranked

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.