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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Network Comparison Type  : Divided

Rank	description	Filtered	red	Interaction Map	Value Type	green	network_comparison
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	4294	High confidence	Ranked	15915	3.70633
	cab2. [refseq;acc:nm_033419]		0.00001		Squared	7.16592	716592
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	16	Low confidence	Ranked	32	2
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	0.00001		Squared	1.87479	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	48.9847		Rooted	23.3131	2.10117
			1362.75		Squared	69.9153	19.4914
			2399.5		Measured	543.5	4.4149
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	19.0788	High confidence	Rooted	0.00001	1907880
				Low confidence
			364	High confidence	Measured		36400000
				Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		5865		Ranked	14977	2.55362
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	10	High confidence		24	2.4
	rad50-interacting protein 1. [refseq;acc:nm_021930]		21.225		Rooted	48.9336	2.30547
			48.0356		Squared	1357.07	28.2513
			450.5		Measured	2394.5	5.31521
2	cab2. [refseq;acc:nm_033419]	0	0.00001			174	17400000
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	48.9847	Low confidence	Rooted	23.3131	2.10117
			1362.75		Squared	69.9153	19.4914
			2399.5		Measured	543.5	4.4149
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	0.00001			89	8900000
					Rooted	9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]				Squared	1.87479	187479
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	223		Ranked	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]		15	High confidence		28	1.86667
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	8906	Low confidence		21883	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		5865	High confidence		14977	2.55362
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		5.61325		Squared	0.00001	561325
			12.4097		Rooted		1240970
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	21.225			48.9336	2.30547
			48.0356		Squared	1357.07	28.2513
			450.5		Measured	2394.5	5.31521
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		223	Low confidence	Ranked	330	1.47982
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		48.9847		Rooted	23.3131	2.10117
			1362.75		Squared	69.9153	19.4914
			2399.5		Measured	543.5	4.4149
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		15	High confidence	Ranked	28	1.86667
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		50.9657		Rooted	26.4292	1.92839
			1596.92		Squared	115.48	13.8285
			2597.5		Measured	698.5	3.71868
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0	0.00001	Low confidence	Squared	1.87479	187479
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]				Measured	89	8900000
					Rooted	9.43398	943398
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]		9607		Ranked	20617	2.14604
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		4475.84	High confidence		11083.9	2.47638
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		0.00001		Measured	109	10900000
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		5.61325		Squared	0.00001	561325
			12.4097		Rooted		1240970
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	223	Low confidence	Ranked	330	1.47982
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		15	High confidence		28	1.86667

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.