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

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Showing element 1 to 50 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	Filtered	description	green	network_comparison	Network Comparison Type	red
1	Measured	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	6325	Subtracted	85
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	36400000	Divided	364
		1	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]	33356.5	8126	Subtracted	41482.5
			rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	5.31521	Divided	450.5
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	3.70633		4294
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	12977	Subtracted	8906
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	107		215
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	2.4	Divided	10
	Squared	0	cab2. [refseq;acc:nm_033419]	7.16592	716592		0.00001
			nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	72283	Subtracted	232467
		1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	145743		468498
			rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	28.2513	Divided	48.0356
	Rooted	0	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	50.8706	Subtracted	9.20014
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	1907880	Divided	19.0788
		1	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	2.30547		21.225
					27.7086	Subtracted
2	Measured	0	cab2. [refseq;acc:nm_033419]	174	17400000	Divided	0.00001
			lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	6325	Subtracted	85
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	8126		41482.5
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	5.31521	Divided	450.5
	Ranked	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	11621	Subtracted	4294
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	2.55362	Divided	5865
		1	hbs1-like. [refseq;acc:nm_006620]	322	107	Subtracted	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]	28	1.86667	Divided	15
	Squared	0	histone h4. [swissprot;acc:p02304]	345123	71500	Subtracted	273623
			nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	561325	Divided	5.61325
		1	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]	263351	143938	Subtracted	407289
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	28.2513	Divided	48.0356
	Rooted	0	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	50.8706	Subtracted	9.20014
			nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	1240970	Divided	12.4097
		1	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	2.30547		21.225
					27.7086	Subtracted
3	Measured	0	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	4196.8		23818.1
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	10900000	Divided	0.00001
		1	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5	8126	Subtracted	41482.5
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	3.71868	Divided	2597.5
	Ranked	0	cab2. [refseq;acc:nm_033419]	10950	10916	Subtracted	21866
			nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	2.47638	Divided	4475.84
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	1.86667		15
			rad50-interacting protein 1. [refseq;acc:nm_021930]	232	105	Subtracted	337
	Squared	0	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	35348		135280
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	561325	Divided	5.61325
		1	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	263351	143938	Subtracted	407289
			homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	13.8285	Divided	1596.92
	Rooted	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	30.0631	Subtracted	36.9188
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	1240970	Divided	12.4097
		1	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	1.92839		50.9657
					24.5365	Subtracted
4	Measured	0	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	8900000	Divided	0.00001
			small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730	3026	Subtracted	18704

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.