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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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

green	Rank	description	Network Comparison Type	red	network_comparison
0	88	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	364	364
	206	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154	154
	207	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	316	ero1-like. [refseq;acc:nm_014584]		82	82
	338	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60	60
	386	dok-like protein. [refseq;acc:nm_024872]		35	35
	429	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		18	18
	494	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	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	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	364	36400000
	20	ero1-like. [refseq;acc:nm_014584]		82	8200000
	22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		60	6000000
	31	dok-like protein. [refseq;acc:nm_024872]		35	3500000
	65	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		18	1800000
	95	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		154	15400000
	96	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	494	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	1
	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	serpin b12. [swissprot;acc:q96p63]		199.549	35.8425
	168		Subtracted		193.982
5.71669	12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	199.249	34.8539
	169		Subtracted		193.532
6.50325	14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	Divided	130.512	20.0687
	258		Subtracted		124.009
11.5	190	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Divided	14	1.21739
	489		Subtracted		2.5
14.3333	121	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	1.3721
	460		Subtracted		5.3334
15	16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Divided	1	15
	443		Subtracted		14
17.6611	21	syntaxin 10 (syn10). [swissprot;acc:o60499]	Divided	118.878	6.73106
	269		Subtracted		101.217
18	64	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	1800000
	428		Subtracted	0	18
19	195	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Divided	23	1.21053
	464		Subtracted		4

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.