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	Filtered	Interaction Map	green	Network Comparison Type	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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

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.