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	Value Type	description	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	Value Type	description	Filtered	green	network_comparison	red
1	Divided	Measured	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	36400000	364
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	2394.5	5.31521	450.5
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	15915	3.70633	4294
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	24	2.4	10
		Squared	cab2. [refseq;acc:nm_033419]	0	7.16592	716592	0.00001
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	1357.07	28.2513	48.0356
		Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	0.00001	1907880	19.0788
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	48.9336	2.30547	21.225
	Subtracted	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	6410	6325	85
			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]	1	33356.5	8126	41482.5
		Ranked	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		322	107	215
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	21883	12977	8906
		Squared	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		160184	72283	232467
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	322755	145743	468498
		Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0	60.0707	50.8706	9.20014
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	48.9336	27.7086	21.225
2	Divided	Measured	cab2. [refseq;acc:nm_033419]	0	174	17400000	0.00001
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	2394.5	5.31521	450.5
		Ranked	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]		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
		Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0.00001	561325	5.61325
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	1357.07	28.2513	48.0356
		Rooted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	0.00001	1240970	12.4097
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	48.9336	2.30547	21.225
	Subtracted	Measured	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		33356.5	8126	41482.5
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	6410	6325	85
		Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		15915	11621	4294
			hbs1-like. [refseq;acc:nm_006620]	1	322	107	215
		Squared	histone h4. [swissprot;acc:p02304]	0	345123	71500	273623
			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]	1	263351	143938	407289
		Rooted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	0	60.0707	50.8706	9.20014
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	48.9336	27.7086	21.225
3	Divided	Measured	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		698.5	3.71868	2597.5
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0	109	10900000	0.00001
		Ranked	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	28	1.86667	15
			nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	11083.9	2.47638	4475.84
		Squared	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	115.48	13.8285	1596.92
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	0.00001	561325	5.61325
		Rooted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	26.4292	1.92839	50.9657
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	0.00001	1240970	12.4097
	Subtracted	Measured	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	33356.5	8126	41482.5
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	0	19621.3	4196.8	23818.1
		Ranked	cab2. [refseq;acc:nm_033419]		10950	10916	21866
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1	232	105	337
		Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	170628	35348	135280
			cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	263351	143938	407289
		Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	6.85565	30.0631	36.9188
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	26.4292	24.5365	50.9657
4	Divided	Measured	hbs1-like. [refseq;acc:nm_006620]		698.5	3.71868	2597.5
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	89	8900000	0.00001

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.