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

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Showing element 1 to 50 of 38536 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

green	Rank	network_comparison	description	Interaction Map	red
0.00001	1	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	364
				Low confidence
	6	1300000	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]		13
	7	231962	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]		2.31962
	20	8200000	ero1-like. [refseq;acc:nm_014584]	High confidence	82
	22	3700000	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	37
		6000000	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	High confidence	60
	23	3700000	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	Low confidence	37
	31	3500000	dok-like protein. [refseq;acc:nm_024872]	High confidence	35
	44	28600000	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	286
	45		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	65	1800000	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	High confidence	18
	95	15400000	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154
	96		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	494	1	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]		0.00001
	495		histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
	496		mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
	497		histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
	498		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
	499		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
	500		rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
	501		h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
	502		brca1 associated protein. [refseq;acc:nm_006768]
	837		gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	Low confidence
	838		gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
	839		cobw-like protein. [refseq;acc:nm_018491]
	840		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
	841		gamma-glutamyltransferase. [sptrembl;acc:q14390]
	842		gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
	843		gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
5.56738	10	35.8425	serpin b12. [swissprot;acc:q96p63]		199.549
	11			High confidence
5.71669		34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Low confidence	199.249
	12			High confidence
6.50325	14	20.0687	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]		130.512
10.6048	9	36.1876	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence	383.762
11.5	176	1.21739	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]		14
	190			High confidence
14.3333	121	1.3721	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]		19.6667
15	16	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]		1
17.5166	5	1751660	jumonji protein. [swissprot;acc:q92833]	Low confidence	0.00001
17.6611	21	6.73106	syntaxin 10 (syn10). [swissprot;acc:o60499]	High confidence	118.878
18	64	1800000	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]		0.00001
19	18	5.21053	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	Low confidence	99
	184	1.21053	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]		23
	195			High confidence
21	50	2.09524	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]		44
23.6984	64	2.03615	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	Low confidence	48.2534
26.1599	18	11.6763	60s ribosomal protein l37a. [swissprot;acc:p12751]	High confidence	305.45
	19		25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]

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.