Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

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Showing element 1 to 50 of 19268 in total

Value Type

: Ranked

Rank	Interaction Map	green	Network Comparison Type	description	Filtered	network_comparison	red
1	High confidence	24	Divided	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	2.4	10
		322	Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	107	215
		15915	Divided	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	3.70633	4294
		21883	Subtracted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	12977	8906
	Low confidence	32	Divided	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]	1	2	16
		330	Subtracted	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	107	223
		14977	Divided	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
		21883	Subtracted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	12977	8906
2	High confidence	28	Divided	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	1.86667	15
		322	Subtracted	hbs1-like. [refseq;acc:nm_006620]	1	107	215
		14977	Divided	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	2.55362	5865
		15915	Subtracted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	11621	4294
	Low confidence	330	Divided	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	1	1.47982	223
		330	Subtracted	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	107	223
		20617	Subtracted	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0	11010	9607
		21883	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	2.45711	8906
3	High confidence	28	Divided	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	1.86667	15
		232	Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	1	105	337
		10950	Subtracted	cab2. [refseq;acc:nm_033419]	0	10916	21866
		11083.9	Divided	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	2.47638	4475.84
	Low confidence	330	Divided	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	1	1.47982	223
		330	Subtracted	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	107	223
		20617	Divided	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	0	2.14604	9607
		20617	Subtracted	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	0	11010	9607
4	High confidence	28	Divided	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	1.86667	15
		232	Subtracted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1	105	337
		21883	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0	2.45711	8906
		21888	Subtracted	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0	10363	11525
	Low confidence	330	Divided	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	1	1.47982	223
		330	Subtracted	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	107	223
		14977	Subtracted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	9112	5865
		20617	Divided	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	0	2.14604	9607
5	High confidence	28	Divided	cytohesin 4. [swissprot;acc:q9uia0]	1	1.86667	15
		309	Subtracted	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	97	212
		11965.7	Divided	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	2.17144	5510.5
		21888	Subtracted	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0	10363	11525
	Low confidence	240	Subtracted	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1	78	318
		330	Divided	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	1	1.47982	223
		13216	Subtracted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	0	9070	22286
		19873	Divided	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	0	1.82499	10889.4
6	High confidence	28	Divided	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1	1.86667	15
		309	Subtracted	protein x 0004. [refseq;acc:nm_016301]	1	97	212
		14977	Subtracted	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	9112	5865
		15339.2	Divided	ubiquitin protein ligase. [refseq;acc:nm_130466]	0	2.03897	7523
	Low confidence	240	Divided	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	1	1.325	318
		240	Subtracted	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	1	78	318
		9583.37	Divided	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	0	1.71877	5575.71
		13216	Subtracted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	0	9070	22286
7	High confidence	212.554	Subtracted	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	1	76.2	288.754
7	High confidence	322	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	1	1.49767	215

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.

- http://analysis.yellowcouch.org/