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

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Showing element 1 to 50 of 77072 in total

Filtered  : 0
green  : 0
Network Comparison Type  : Subtracted

description	red	network_comparison	Value Type	Interaction Map	Rank
brca1 associated protein. [refseq;acc:nm_006768]	0	0	Measured	High confidence	502
			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	0.324024	Squared	Low confidence	826
	6.08276	6.08276	Rooted		42
	37	37	Measured		648
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	0.324024	0.324024	Squared		827
	6.08276	6.08276	Rooted		43
	37	37	Measured		649
cobw-like protein. [refseq;acc:nm_018491]	0	0			839
			Ranked
			Squared
			Rooted
dok-like protein. [refseq;acc:nm_024872]	0.289941	0.289941	Squared	High confidence	467
	5.91608	5.91608	Rooted		74
	35	35	Measured		386
ero1-like. [refseq;acc:nm_014584]	1.59148	1.59148	Squared		440
	9.05539	9.05539	Rooted		38
	82	82	Measured		316
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	0	0		Low confidence	838
			Ranked
			Squared
			Rooted
gamma-glutamyltransferase. [sptrembl;acc:q14390]			Measured		841
			Ranked
			Squared
			Rooted
gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]			Measured		842
			Ranked
			Squared
			Rooted
gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]			Measured		837
			Ranked
			Squared
			Rooted
gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]			Measured		843
			Ranked
			Squared
			Rooted
h2a histone family, member j isoform 1. [refseq;acc:nm_018267]			Measured	High confidence	501
			Squared
			Rooted
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]			Measured		495
			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]			Measured		494
			Squared
			Rooted
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]			Measured		497

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.