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	Interaction Map	Value Type	Filtered	Network Comparison Type	green	red	network_comparison

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Showing element 1 to 50 of 19268 in total

Value Type  : Ranked

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

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.