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

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

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

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.