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

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Showing element 1 to 50 of 77072 in total

Network Comparison Type  : Divided

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

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.