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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

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