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

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Showing element 1 to 50 of 19268 in total

Value Type  : Ranked

Rank	description	Interaction Map	Network Comparison Type	Filtered	network_comparison	green	red
1	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	High confidence	Divided	0	3.70633	15915	4294
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	Low confidence		1	2	32	16
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	High confidence	Subtracted		107	322	215
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence				330	223
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence		0	12977	21883	8906
		Low confidence
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		Divided		2.55362	14977	5865
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	High confidence		1	2.4	24	10
2	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		Subtracted	0	11621	15915	4294
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence		1	107	330	223
	hbs1-like. [refseq;acc:nm_006620]	High confidence				322	215
	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Low confidence	Divided		1.47982	330	223
	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			1.86667	28	15
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Low confidence		0	2.45711	21883	8906
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence			2.55362	14977	5865
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence	Subtracted		11010	20617	9607
3	cab2. [refseq;acc:nm_033419]	High confidence			10916	10950	21866
	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Low confidence	Divided	1	1.47982	330	223
	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]		Subtracted		107
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	High confidence	Divided		1.86667	28	15
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Low confidence		0	2.14604	20617	9607
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Subtracted		11010
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	High confidence	Divided		2.47638	11083.9	4475.84
	rad50-interacting protein 1. [refseq;acc:nm_021930]		Subtracted	1	105	232	337
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Low confidence	Divided		1.47982	330	223
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	High confidence			1.86667	28	15
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Low confidence	Subtracted		107	330	223
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	High confidence	Divided	0	2.45711	21883	8906
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Low confidence	Subtracted		9112	14977	5865
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]		Divided		2.14604	20617	9607
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	High confidence	Subtracted		10363	21888	11525
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]			1	105	232	337
5	cytohesin 4. [swissprot;acc:q9uia0]		Divided		1.86667	28	15
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Low confidence	Subtracted	0	9070	13216	22286
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		Divided	1	1.47982	330	223
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Subtracted		78	240	318
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	High confidence		0	10363	21888	11525
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		Divided		2.17144	11965.7	5510.5
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	Low confidence			1.82499	19873	10889.4
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	High confidence	Subtracted	1	97	309	212
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Divided		1.86667	28	15
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Low confidence	Subtracted	0	9070	13216	22286
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	High confidence			9112	14977	5865
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Low confidence		1	78	240	318
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Divided		1.325
	protein x 0004. [refseq;acc:nm_016301]	High confidence	Subtracted		97	309	212
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Low confidence	Divided	0	1.71877	9583.37	5575.71
	ubiquitin protein ligase. [refseq;acc:nm_130466]	High confidence			2.03897	15339.2	7523
7	cab2. [refseq;acc:nm_033419]				1.99689	10950	21866
	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Low confidence			1.69451	6812	11543

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.