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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 16578 in total

Value Type	Ranked
Filtered	1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison	
1	CPD	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Divided	Low confidence	16	32	2	
1	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	High confidence	215	322	107	
1	LAMP1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Subtracted	Low confidence	223	330	107	
1	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	High confidence	10	24	2.4	
2		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). [source:swissprot;acc:o60476]	Divided	High confidence	15	28	1.86667	
2	CDK4	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Subtracted	Low confidence	223	330	107	
2	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	High confidence	215	322	107	
2	LAMP1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Divided	Low confidence	223	330	1.47982	
3	CDK4	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Divided	Low confidence	223	330	1.47982	
3	CDK6	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Subtracted	Low confidence	223	330	107	
3	PSCD1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	High confidence	15	28	1.86667	
3	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	High confidence	337	232	105	
4	CDK6	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Divided	Low confidence	223	330	1.47982	
4	LAMP2	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Subtracted	Low confidence	223	330	107	
4	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	High confidence	15	28	1.86667	
4	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	High confidence	337	232	105	
5	LAMP2	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Divided	Low confidence	223	330	1.47982	
5	OSBPL6	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Subtracted	Low confidence	318	240	78	
5	PSCD4	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	High confidence	15	28	1.86667	
5	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	High confidence	212	309	97	
6	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	High confidence	212	309	97	
6	OSBPL3	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Subtracted	Low confidence	318	240	78	
6	OSBPL6	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Divided	Low confidence	318	240	1.325	
6	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	High confidence	15	28	1.86667	
7	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	High confidence	215	322	1.49767	
7	OSBPL3	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Divided	Low confidence	318	240	1.325	
7	OSBPL7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Subtracted	Low confidence	318	240	78	
7	UFC1	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Subtracted	High confidence	288.754	212.554	76.2	
8	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Divided	High confidence	215	322	1.49767	
8	JMJD1C	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Subtracted	Low confidence	305.472	247.246	58.226	
8	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Subtracted	High confidence	288	362	74	
8	OSBPL7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Divided	Low confidence	318	240	1.325	
9	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Subtracted	High confidence	288	362	74	
9	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Divided	Low confidence	58	44	1.31818	
9	TMEM132A	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	Low confidence	305.399	247.213	58.186	
9	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Divided	High confidence	212	309	1.45755	
10	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	Divided	High confidence	212	309	1.45755	
10	JMJD1A	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Subtracted	Low confidence	305.303	247.169	58.134	
10	SLC25A43	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Divided	Low confidence	58	44	1.31818	
10	SMPD2	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	Subtracted	High confidence	288	362	74	
11	BEST1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Divided	Low confidence	37.318	28.4944	1.30966	
11	PRSS3	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Subtracted	Low confidence	304.548	246.824	57.724	
11	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	High confidence	337	232	1.45259	
11	TMEM33	db83 protein. [source:swissprot;acc:p57088]	Subtracted	High confidence	288	362	74	
12		guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Subtracted	High confidence	266.856	336.233	69.377	
12	BEST4	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Divided	Low confidence	37.3475	28.5242	1.30933	
12	PRSS1	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Subtracted	Low confidence	304.359	246.737	57.622	
12	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	High confidence	337	232	1.45259	
13		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Divided	Low confidence	37.9984	29.1831	1.30207	
13	GNG12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	Subtracted	High confidence	266.856	336.233	69.377	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/