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	Value Type	network_comparison	red	Gene	Interaction Map	Rank	Network Comparison Type

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Showing element 101 to 150 of 77072 in total

Filtered  : 0
green  : 0.00001
Network Comparison Type  : Divided

description	Value Type	network_comparison	red	Interaction Map	Rank
brca1 associated protein. [refseq;acc:nm_006768]	Squared	1	0.00001	High confidence	502
	Rooted
carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	Measured	3700000	37	Low confidence	22
	Squared	32402.4	0.324024		5
	Rooted	608276	6.08276		6
carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Measured	3700000	37		23
	Squared	32402.4	0.324024		6
	Rooted	608276	6.08276		7
cobw-like protein. [refseq;acc:nm_018491]	Measured	1	0.00001		839
	Ranked
	Squared
	Rooted
dok-like protein. [refseq;acc:nm_024872]	Measured	3500000	35	High confidence	31
	Squared	28994.1	0.289941		13
	Rooted	591608	5.91608
ero1-like. [refseq;acc:nm_014584]	Measured	8200000	82		20
	Squared	159148	1.59148		8
	Rooted	905539	9.05539
gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	Measured	1	0.00001	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
	Squared
	Rooted

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.