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

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Showing element 1 to 50 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	green	description	Network Comparison Type	Interaction Map	network_comparison	red
1	24	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Divided	High confidence	2.4	10
	32	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		Low confidence	2	16
	322	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	High confidence	107	215
	330	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]		Low confidence		223
2	28	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]	Divided	High confidence	1.86667	15
	322	hbs1-like. [refseq;acc:nm_006620]	Subtracted		107	215
	330	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]		Low confidence		223
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Divided		1.47982
3	28	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]		High confidence	1.86667	15
	232	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted		105	337
	330	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	Divided	Low confidence	1.47982	223
		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Subtracted		107
4	28	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Divided	High confidence	1.86667	15
	232	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted		105	337
	330	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	Divided	Low confidence	1.47982	223
		lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Subtracted		107
5	28	cytohesin 4. [swissprot;acc:q9uia0]	Divided	High confidence	1.86667	15
	240	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Subtracted	Low confidence	78	318
	309	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		High confidence	97	212
	330	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	Low confidence	1.47982	223
6	28	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		High confidence	1.86667	15
	240	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Subtracted	Low confidence	78	318
		oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Divided		1.325
	309	protein x 0004. [refseq;acc:nm_016301]	Subtracted	High confidence	97	212
7	212.554	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]			76.2	288.754
	240	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided	Low confidence	1.325	318
		oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]	Subtracted		78
	322	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	High confidence	1.49767	215
8	240	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2]		Low confidence	1.325	318
	247.246	thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652]	Subtracted		58.226	305.472
	322	hbs1-like. [refseq;acc:nm_006620]	Divided	High confidence	1.49767	215
	362	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Subtracted		74	288
9	44	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Divided	Low confidence	1.31818	58
	247.213	gbp protein isoform a. [refseq;acc:nm_017870]	Subtracted		58.186	305.399
	309	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Divided	High confidence	1.45755	212
	362	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Subtracted		74	288
10	44	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Divided	Low confidence	1.31818	58
	247.169	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433]	Subtracted		58.134	305.303
	309	protein x 0004. [refseq;acc:nm_016301]	Divided	High confidence	1.45755	212
	362	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Subtracted		74	288
11	28.4944	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Divided	Low confidence	1.30966	37.318
	232	rad50-interacting protein 1. [refseq;acc:nm_021930]		High confidence	1.45259	337
	246.824	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030]	Subtracted	Low confidence	57.724	304.548
	362	db83 protein. [swissprot;acc:p57088]		High confidence	74	288
12	28.5242	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	Divided	Low confidence	1.30933	37.3475
	232	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		High confidence	1.45259	337
	246.737	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]	Subtracted	Low confidence	57.622	304.359
	336.233	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		High confidence	69.377	266.856
13	29.1831	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	Low confidence	1.30207	37.9984
	202.362	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted		52.684	255.046

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.