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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 2116 in total

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

Rank	Interaction Map	Value Type	description
494	High confidence	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
837	Low confidence	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.