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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided

Rank	Value Type	Interaction Map	description	red	green	Filtered	network_comparison
1	Measured	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	0	36400000
			rad50-interacting protein 1. [refseq;acc:nm_021930]	450.5	2394.5	1	5.31521
		Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	2399.5	543.5		4.4149
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	0.00001	0	36400000
	Ranked	High confidence	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	4294	15915		3.70633
			putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	10	24	1	2.4
		Low confidence	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	16	32		2
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	14977	0	2.55362
	Squared	High confidence	cab2. [refseq;acc:nm_033419]	0.00001	7.16592		716592
			rad50-interacting protein 1. [refseq;acc:nm_021930]	48.0356	1357.07	1	28.2513
		Low confidence	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	1.87479	0	187479
			lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1362.75	69.9153	1	19.4914
	Rooted	High confidence	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	0.00001	0	1907880
			rad50-interacting protein 1. [refseq;acc:nm_021930]	21.225	48.9336	1	2.30547
		Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	48.9847	23.3131		2.10117
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	19.0788	0.00001	0	1907880
2	Measured	High confidence	cab2. [refseq;acc:nm_033419]	0.00001	174		17400000
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	450.5	2394.5	1	5.31521
		Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	2399.5	543.5		4.4149
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	0	8900000
	Ranked	High confidence	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	28	1	1.86667
			mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	5865	14977	0	2.55362
		Low confidence	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	223	330	1	1.47982
			mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	8906	21883	0	2.45711
	Squared	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	5.61325	0.00001		561325
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.0356	1357.07	1	28.2513
		Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1362.75	69.9153		19.4914
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	1.87479	0	187479
	Rooted	High confidence	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	12.4097	0.00001		1240970
			rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	21.225	48.9336	1	2.30547
		Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	48.9847	23.3131		2.10117
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	9.43398	0	943398
3	Measured	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	2597.5	698.5	1	3.71868
			pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	0.00001	109	0	10900000
		Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	2399.5	543.5	1	4.4149
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	89	0	8900000
	Ranked	High confidence	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	15	28	1	1.86667
			nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	4475.84	11083.9	0	2.47638
		Low confidence	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	223	330	1	1.47982
			neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	9607	20617	0	2.14604
	Squared	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1596.92	115.48	1	13.8285
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	5.61325	0.00001	0	561325
		Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1362.75	69.9153	1	19.4914
			homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	0.00001	1.87479	0	187479
	Rooted	High confidence	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	50.9657	26.4292	1	1.92839
			transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	12.4097	0.00001	0	1240970
		Low confidence	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	48.9847	23.3131	1	2.10117
			homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0.00001	9.43398	0	943398
4	Measured	High confidence	hbs1-like. [refseq;acc:nm_006620]	2597.5	698.5	1	3.71868
			homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0.00001	89	0	8900000

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.