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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

green  : 0
Filtered  : 0
Network Comparison Type  : Subtracted

description	red	Rank	Interaction Map	Value Type	network_comparison
brca1 associated protein. [refseq;acc:nm_006768]	0	502	High confidence	Measured	0
				Ranked
				Squared
				Rooted
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	0.324024	826	Low confidence	Squared	0.324024
	6.08276	42		Rooted	6.08276
	37	648		Measured	37
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	0.324024	827		Squared	0.324024
	6.08276	43		Rooted	6.08276
	37	649		Measured	37
cobw-like protein. [refseq;acc:nm_018491]	0	839			0
				Ranked
				Squared
				Rooted
dok-like protein. [refseq;acc:nm_024872]	0.289941	467	High confidence	Squared	0.289941
	5.91608	74		Rooted	5.91608
	35	386		Measured	35
ero1-like. [refseq;acc:nm_014584]	1.59148	440		Squared	1.59148
	9.05539	38		Rooted	9.05539
	82	316		Measured	82
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	0	838	Low confidence		0
				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
h2a histone family, member j isoform 1. [refseq;acc:nm_018267]		501	High confidence	Measured
				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

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.