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	Network Comparison Type	Value Type	Interaction Map	red	Filtered	green	network_comparison

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

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

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.