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

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Showing element 1 to 50 of 19268 in total

Value Type

: Ranked

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

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/