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

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

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.