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

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Showing element 1 to 50 of 77072 in total

Rank	Network Comparison Type	Value Type	Interaction Map	description	green	red	Filtered	network_comparison
1	Divided	Measured	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	0	36400000
				rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	450.5	1	5.31521
			Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	543.5	2399.5		4.4149
				mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	0	36400000
		Ranked	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294		3.70633
				putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	10	1	2.4
			Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	32	16		2
				mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865	0	2.55362
		Squared	High confidence	cab2. [refseq;acc:nm_033419]	7.16592	0.00001		716592
				rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	48.0356	1	28.2513
			Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	1.87479	0.00001	0	187479
				lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	69.9153	1362.75	1	19.4914
		Rooted	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	19.0788	0	1907880
				rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	1	2.30547
			Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	23.3131	48.9847		2.10117
				mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	19.0788	0	1907880
	Subtracted	Measured	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85		6325
				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	41482.5	1	8126
			Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	0	6325
				carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	32028.5	40899	1	8870.5
		Ranked	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	215		107
				mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906	0	12977
			Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	330	223	1	107
				mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906	0	12977
		Squared	High confidence	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	232467		72283
				putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	468498	1	145743
			Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	242799	395912		153113
				nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	232467	0	72283
		Rooted	High confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	9.20014		50.8706
				rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	1	27.7086
			Low confidence	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	9.20014	0	50.8706
				lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	23.3131	48.9847	1	25.6716
2	Divided	Measured	High confidence	cab2. [refseq;acc:nm_033419]	174	0.00001	0	17400000
				rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	450.5	1	5.31521
			Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	543.5	2399.5		4.4149
				homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001	0	8900000
		Ranked	High confidence	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	15	1	1.86667
				mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865	0	2.55362
			Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	330	223	1	1.47982
				mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906	0	2.45711
		Squared	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	5.61325		561325
				rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	48.0356	1	28.2513
			Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	69.9153	1362.75		19.4914
				homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	1.87479	0.00001	0	187479
		Rooted	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	12.4097		1240970
				rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	21.225	1	2.30547
			Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	23.3131	48.9847		2.10117
				homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	9.43398	0.00001	0	943398
	Subtracted	Measured	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	41482.5	1	8126
				lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	85	0	6325

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.