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	Value Type	Gene	description	network_comparison	Interaction Map	red	Rank	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

Value Type	description	network_comparison	Interaction Map	red	Rank
Measured	brca1 associated protein. [refseq;acc:nm_006768]	1	High confidence	0.00001	502
	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	3700000	Low confidence	37	22
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]				23
	cobw-like protein. [refseq;acc:nm_018491]	1		0.00001	839
	dok-like protein. [refseq;acc:nm_024872]	3500000	High confidence	35	31
	ero1-like. [refseq;acc:nm_014584]	8200000		82	20
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	1	Low confidence	0.00001	838
	gamma-glutamyltransferase. [sptrembl;acc:q14390]				841
	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]				842
	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]				837
	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]				843
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]		High confidence		501
	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]				495
	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
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]				497
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]				499
		1300000	Low confidence	13	6
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	High confidence	364	1
			Low confidence
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	1	High confidence	0.00001	496
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	28600000	Low confidence	286	44
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]				45
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	15400000	High confidence	154	95
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	1800000		18	65
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	1		0.00001	500
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	6000000		60	22
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	231962	Low confidence	2.31962	7
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	15400000	High confidence	154	96
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	1		0.00001	498
			Low confidence		840
Ranked	brca1 associated protein. [refseq;acc:nm_006768]		High confidence		502
	cobw-like protein. [refseq;acc:nm_018491]		Low confidence		839
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]				838
	gamma-glutamyltransferase. [sptrembl;acc:q14390]				841
	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]				842
	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]				837
	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]				843
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		High confidence		501
Squared	brca1 associated protein. [refseq;acc:nm_006768]				502
	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	32402.4	Low confidence	0.324024	5
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]				6
	cobw-like protein. [refseq;acc:nm_018491]	1		0.00001	839
	dok-like protein. [refseq;acc:nm_024872]	28994.1	High confidence	0.289941	13
	ero1-like. [refseq;acc:nm_014584]	159148		1.59148	8
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	1	Low confidence	0.00001	838
	gamma-glutamyltransferase. [sptrembl;acc:q14390]				841
	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]				842
	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]				837
	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]				843
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]		High confidence		501

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.