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	Rank	Gene	description	network_comparison	Network Comparison Type	Interaction Map	red

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Showing element 51 to 100 of 77072 in total

Filtered  : 0
Value Type  : Measured

green	Rank	description	network_comparison	Network Comparison Type	Interaction Map	red
0.00001	500	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	1	Divided	High confidence	0.00001
	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	serpin b12. [swissprot;acc:q96p63]	35.8425			199.549
	11				High confidence
	168		193.982	Subtracted
	280				Low confidence
5.71669	11	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	Divided		199.249
	12				High confidence
	169		193.532	Subtracted
	281				Low confidence
6.50325	14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20.0687	Divided	High confidence	130.512
	258		124.009	Subtracted
10.6048	9	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	36.1876	Divided	Low confidence	383.762
	166		373.157	Subtracted
11.5	176	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	1.21739	Divided		14
	190				High confidence
	489		2.5	Subtracted
	819				Low confidence
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]	1.3721	Divided	High confidence	19.6667
	460		5.3334	Subtracted
15	16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	Divided		1
	443		14	Subtracted
17.5166	5	jumonji protein. [swissprot;acc:q92833]	1751660	Divided	Low confidence	0.00001
	755		17.5166	Subtracted		0
17.6611	21	syntaxin 10 (syn10). [swissprot;acc:o60499]	6.73106	Divided	High confidence	118.878
	269		101.217	Subtracted
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]	1800000	Divided		0.00001
	428		18	Subtracted		0
19	18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	5.21053	Divided	Low confidence	99
	184	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	1.21053			23
	195				High confidence
	464		4	Subtracted
	483	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	80		Low confidence	99
	807	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	4			23
21	50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	2.09524	Divided	High confidence	44
	407		23	Subtracted
23.6984	64	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	2.03615	Divided	Low confidence	48.2534
	713		24.555	Subtracted
26.1599	18	60s ribosomal protein l37a. [swissprot;acc:p12751]	11.6763	Divided	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]
	114	60s ribosomal protein l37a. [swissprot;acc:p12751]	279.29	Subtracted
	115	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.