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

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	network_comparison	red	green
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked	Divided	0	3.70633	4294	15915
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Measured	Subtracted		6325	85	6410
		Rooted			50.8706	9.20014	60.0707
	cab2. [refseq;acc:nm_033419]	Squared	Divided		716592	0.00001	7.16592
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Ranked	Subtracted	1	107	215	322
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured			8126	41482.5	33356.5
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Divided	0	36400000	364	0.00001
		Ranked	Subtracted		12977	8906	21883
		Rooted	Divided		1907880	19.0788	0.00001
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared	Subtracted		72283	232467	160184
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Ranked	Divided	1	2.4	10	24
		Squared	Subtracted		145743	468498	322755
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	Divided		5.31521	450.5	2394.5
		Squared			28.2513	48.0356	1357.07
		Rooted			2.30547	21.225	48.9336
			Subtracted		27.7086
2	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked		0	11621	4294	15915
	cab2. [refseq;acc:nm_033419]	Measured	Divided		17400000	0.00001	174
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Subtracted	1	8126	41482.5	33356.5
	hbs1-like. [refseq;acc:nm_006620]	Ranked			107	215	322
	histone h4. [swissprot;acc:p02304]	Squared		0	71500	273623	345123
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured			6325	85	6410
		Rooted			50.8706	9.20014	60.0707
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Ranked	Divided	1	1.86667	15	28
		Squared	Subtracted		143938	407289	263351
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Ranked	Divided	0	2.55362	5865	14977
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared			561325	5.61325	0.00001
		Rooted			1240970	12.4097
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured		1	5.31521	450.5	2394.5
		Squared			28.2513	48.0356	1357.07
		Rooted			2.30547	21.225	48.9336
			Subtracted		27.7086
3	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]			0	30.0631	36.9188	6.85565
	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Squared			35348	135280	170628
	cab2. [refseq;acc:nm_033419]	Ranked			10916	21866	10950
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		Divided	1	1.86667	15	28
		Squared	Subtracted		143938	407289	263351
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured			8126	41482.5	33356.5
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Divided		3.71868	2597.5	698.5
		Squared			13.8285	1596.92	115.48
		Rooted			1.92839	50.9657	26.4292
			Subtracted		24.5365
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	Divided	0	2.47638	4475.84	11083.9
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	Subtracted		4196.8	23818.1	19621.3
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		Divided		10900000	0.00001	109
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Subtracted	1	105	337	232
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	Divided	0	561325	5.61325	0.00001
		Rooted			1240970	12.4097
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked		1	1.86667	15	28
		Squared	Subtracted		143938	407289	263351

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.