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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Rank	green	description	red	Network Comparison Type	Filtered	Value Type	Interaction Map	network_comparison
1	0.00001	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	Divided	0	Rooted	High confidence	1907880
							Low confidence
			364			Measured	High confidence	36400000
							Low confidence
	1.87479	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001			Squared		187479
	7.16592	cab2. [refseq;acc:nm_033419]					High confidence	716592
	23.3131	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	48.9847		1	Rooted	Low confidence	2.10117
				Subtracted				25.6716
	24	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	Divided		Ranked	High confidence	2.4
	32	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	16				Low confidence	2
	48.9336	rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225			Rooted	High confidence	2.30547
				Subtracted				27.7086
	60.0707	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9.20014		0			50.8706
							Low confidence
	69.9153	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1362.75	Divided	1	Squared		19.4914
	322	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	215	Subtracted		Ranked	High confidence	107
	330	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	223				Low confidence
	543.5		2399.5	Divided		Measured		4.4149
	1357.07	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.0356			Squared	High confidence	28.2513
	2394.5		450.5			Measured		5.31521
	6410	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	85	Subtracted	0			6325
							Low confidence
	14977	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	Divided		Ranked		2.55362
	15915	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294				High confidence	3.70633
	21883	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	Subtracted				12977
							Low confidence
	32028.5	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	40899		1	Measured		8870.5
	33356.5	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]	41482.5				High confidence	8126
	160184	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	232467		0	Squared		72283
							Low confidence
	242799	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	395912		1			153113
	322755	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	468498				High confidence	145743
2	0.00001	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	Divided	0			561325
			12.4097			Rooted		1240970
	1.87479	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001			Squared	Low confidence	187479
	7.61577	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	29.3087	Subtracted		Rooted		21.6929
	9.43398	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	Divided				943398
	23.3131	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	48.9847		1			2.10117
				Subtracted				25.6716
	28	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]	15	Divided		Ranked	High confidence	1.86667
	48.9336	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225			Rooted		2.30547
				Subtracted				27.7086
	60.0707	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	9.20014		0			50.8706
	69.9153	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1362.75	Divided	1	Squared	Low confidence	19.4914
	89	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001		0	Measured		8900000
	174	cab2. [refseq;acc:nm_033419]					High confidence	17400000
	322	hbs1-like. [refseq;acc:nm_006620]	215	Subtracted	1	Ranked		107
	330	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	223				Low confidence
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Divided				1.47982
	543.5	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2399.5			Measured		4.4149

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.