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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	Value Type	description	Interaction Map	Network Comparison Type	green	network_comparison	Filtered	red
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	High confidence	Subtracted	6410	6325	0	85
			Low confidence
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			32028.5	8870.5	1	40899
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Divided	543.5	4.4149		2399.5
		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]	High confidence	Subtracted	33356.5	8126		41482.5
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Divided	0.00001	36400000	0	364
			Low confidence
		rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence		2394.5	5.31521	1	450.5
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]			15915	3.70633	0	4294
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence		32	2	1	16
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	Subtracted	322	107		215
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence		330			223
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence		21883	12977	0	8906
			Low confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Divided	14977	2.55362		5865
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence		24	2.4	1	10
	Squared	cab2. [refseq;acc:nm_033419]			7.16592	716592	0	0.00001
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence	Subtracted	242799	153113	1	395912
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Divided	1.87479	187479	0	0.00001
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]			69.9153	19.4914	1	1362.75
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	High confidence	Subtracted	160184	72283	0	232467
			Low confidence
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence		322755	145743	1	468498
		rad50-interacting protein 1. [refseq;acc:nm_021930]		Divided	1357.07	28.2513		48.0356
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Subtracted	60.0707	50.8706	0	9.20014
			Low confidence
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Divided	23.3131	2.10117	1	48.9847
				Subtracted		25.6716
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Divided	0.00001	1907880	0	19.0788
			Low confidence
		rad50-interacting protein 1. [refseq;acc:nm_021930]	High confidence		48.9336	2.30547	1	21.225
				Subtracted		27.7086
2	Measured	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Low confidence		28492	7307		21185
		cab2. [refseq;acc:nm_033419]	High confidence	Divided	174	17400000	0	0.00001
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence		543.5	4.4149	1	2399.5
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	Subtracted	33356.5	8126		41482.5
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	Divided	89	8900000	0	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	High confidence	Subtracted	6410	6325		85
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Low confidence		19621.3	4196.8		23818.1
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	High confidence	Divided	2394.5	5.31521	1	450.5
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		Subtracted	15915	11621	0	4294
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence		330	107	1	223
		hbs1-like. [refseq;acc:nm_006620]	High confidence		322			215
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	Divided	330	1.47982		223
		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]	High confidence		28	1.86667		15
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Low confidence		21883	2.45711	0	8906
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence		14977	2.55362		5865
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	Subtracted	20617	11010		9607
	Squared	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]			475119	141563	1	333556
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Divided	69.9153	19.4914		1362.75

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.