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

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Showing element 1 to 50 of 77072 in total

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Network Comparison Type  : Subtracted

description	green	Rank	Interaction Map	Value Type	network_comparison
brca1 associated protein. [refseq;acc:nm_006768]	0	502	High confidence	Measured	0
				Ranked
				Squared
				Rooted
cab2. [refseq;acc:nm_033419]	7.16592	402		Squared	7.16592
	13.1909	13		Rooted	13.1909
	174	185		Measured	174
cobw-like protein. [refseq;acc:nm_018491]	0	839	Low confidence		0
				Ranked
				Squared
				Rooted
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]		838		Measured
				Ranked
				Squared
				Rooted
gamma-glutamyltransferase. [sptrembl;acc:q14390]		841		Measured
				Ranked
				Squared
				Rooted
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]		842		Measured
				Ranked
				Squared
				Rooted
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]		837		Measured
				Ranked
				Squared
				Rooted
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]		843		Measured
				Ranked
				Squared
				Rooted
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0.823905	450	High confidence	Squared	0.823905
		804	Low confidence
	7.68115	26		Rooted	7.68115
		52	High confidence
	59	342		Measured	59
		554	Low confidence
h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	0	501	High confidence		0
				Squared
				Rooted
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]		495		Measured
				Squared
				Rooted
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]		494		Measured
				Squared
				Rooted
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]		497		Measured
				Squared
				Rooted
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	439		Squared	1.87479

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.