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

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Showing element 1 to 50 of 2116 in total

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

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