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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Value Type  : Measured
Filtered  : 0
Interaction Map  : High confidence

green	Rank	network_comparison	description	Network Comparison Type	red
0	88	364	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	364
	206	154	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154
	207		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	316	82	ero1-like. [refseq;acc:nm_014584]		82
	338	60	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60
	386	35	dok-like protein. [refseq;acc:nm_024872]		35
	429	18	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		18
	494	0	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
	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]
0.00001	1	36400000	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364
	20	8200000	ero1-like. [refseq;acc:nm_014584]		82
	22	6000000	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60
	31	3500000	dok-like protein. [refseq;acc:nm_024872]		35
	65	1800000	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		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]
5.56738	11	35.8425	serpin b12. [swissprot;acc:q96p63]		199.549
	168	193.982		Subtracted
5.71669	12	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	199.249
	169	193.532		Subtracted
6.50325	14	20.0687	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	130.512
	258	124.009		Subtracted
11.5	190	1.21739	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Divided	14
	489	2.5		Subtracted
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]	Divided	19.6667
	460	5.3334		Subtracted
15	16	15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Divided	1
	443	14		Subtracted
17.6611	21	6.73106	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	118.878
	269	101.217		Subtracted
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]	Divided	0.00001
	428	18		Subtracted	0
19	195	1.21053	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Divided	23
	464	4		Subtracted

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.