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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	Network Comparison Type	description	Filtered	Interaction Map	Value Type	red	network_comparison	green
1	Divided	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	High confidence	Ranked	4294	3.70633	15915
		cab2. [refseq;acc:nm_033419]			Squared	0.00001	716592	7.16592
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	Low confidence	Ranked	16	2	32
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0		Squared	0.00001	187479	1.87479
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1		Measured	2399.5	4.4149	543.5
					Squared	1362.75	19.4914	69.9153
					Rooted	48.9847	2.10117	23.3131
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	High confidence	Measured	364	36400000	0.00001
					Rooted	19.0788	1907880
				Low confidence	Measured	364	36400000
					Rooted	19.0788	1907880
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]			Ranked	5865	2.55362	14977
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	High confidence		10	2.4	24
		rad50-interacting protein 1. [refseq;acc:nm_021930]			Measured	450.5	5.31521	2394.5
					Squared	48.0356	28.2513	1357.07
					Rooted	21.225	2.30547	48.9336
	Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	0		Measured	85	6325	6410
					Rooted	9.20014	50.8706	60.0707
				Low confidence	Measured	85	6325	6410
					Rooted	9.20014	50.8706	60.0707
		carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1		Measured	40899	8870.5	32028.5
					Squared	395912	153113	242799
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		High confidence	Ranked	215	107	322
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Low confidence		223		330
					Rooted	48.9847	25.6716	23.3131
		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	Measured	41482.5	8126	33356.5
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0		Ranked	8906	12977	21883
				Low confidence
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		High confidence	Squared	232467	72283	160184
				Low confidence
		putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	High confidence		468498	145743	322755
		rad50-interacting protein 1. [refseq;acc:nm_021930]			Rooted	21.225	27.7086	48.9336
2	Divided	cab2. [refseq;acc:nm_033419]	0		Measured	0.00001	17400000	174
		cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	Low confidence		2399.5	4.4149	543.5
					Squared	1362.75	19.4914	69.9153
					Rooted	48.9847	2.10117	23.3131
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0		Measured	0.00001	8900000	89
					Rooted		943398	9.43398
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]			Squared		187479	1.87479
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1		Ranked	223	1.47982	330
		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	1.86667	28
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	Low confidence		8906	2.45711	21883
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		High confidence		5865	2.55362	14977
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]			Squared	5.61325	561325	0.00001
					Rooted	12.4097	1240970
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1		Measured	450.5	5.31521	2394.5
					Squared	48.0356	28.2513	1357.07
					Rooted	21.225	2.30547	48.9336
	Subtracted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Low confidence	Measured	21185	7307	28492
		adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	High confidence	Ranked	4294	11621	15915

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.