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 Network Comparison Type description Filtered Interaction Map network_comparison red green

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Showing element 1 to 50 of 19268 in total

Value Type

: Ranked

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

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/