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	Interaction Map	Value Type	Gene	network_comparison	Rank	red	Network Comparison Type

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
green  : 0.00001
Network Comparison Type  : Divided

description	Interaction Map	Value Type	network_comparison	Rank	red
brca1 associated protein. [refseq;acc:nm_006768]	High confidence	Measured	1	502	0.00001
		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]	Low confidence	Measured	3700000	22	37
		Squared	32402.4	5	0.324024
		Rooted	608276	6	6.08276
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]		Measured	3700000	23	37
		Squared	32402.4	6	0.324024
		Rooted	608276	7	6.08276
cobw-like protein. [refseq;acc:nm_018491]		Measured	1	839	0.00001
		Ranked
		Squared
		Rooted
dok-like protein. [refseq;acc:nm_024872]	High confidence	Measured	3500000	31	35
		Squared	28994.1	13	0.289941
		Rooted	591608		5.91608
ero1-like. [refseq;acc:nm_014584]		Measured	8200000	20	82
		Squared	159148	8	1.59148
		Rooted	905539		9.05539
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	Low confidence	Measured	1	838	0.00001
		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]	High confidence	Measured		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.