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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 66312 in total

Filtered	1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	network_comparison	green	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Measured	Subtracted	Low confidence	40899	8870.5	32028.5	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Ranked	Divided	Low confidence	16	2	32	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Squared	Subtracted	Low confidence	395912	153113	242799	
1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	Subtracted	High confidence	215	107	322	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Measured	Divided	Low confidence	2399.5	4.4149	543.5	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Ranked	Subtracted	Low confidence	223	107	330	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Squared	Divided	Low confidence	1362.75	19.4914	69.9153	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Rooted	Divided	Low confidence	48.9847	2.10117	23.3131	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Rooted	Subtracted	Low confidence	48.9847	25.6716	23.3131	
1	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]	Measured	Subtracted	High confidence	41482.5	8126	33356.5	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Ranked	Divided	High confidence	10	2.4	24	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Squared	Subtracted	High confidence	468498	145743	322755	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	Divided	High confidence	450.5	5.31521	2394.5	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Squared	Divided	High confidence	48.0356	28.2513	1357.07	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	Divided	High confidence	21.225	2.30547	48.9336	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	Subtracted	High confidence	21.225	27.7086	48.9336	
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Measured	Subtracted	Low confidence	21185	7307	28492	
2	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Squared	Subtracted	Low confidence	333556	141563	475119	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Measured	Divided	Low confidence	2399.5	4.4149	543.5	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Ranked	Subtracted	Low confidence	223	107	330	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Squared	Divided	Low confidence	1362.75	19.4914	69.9153	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Rooted	Divided	Low confidence	48.9847	2.10117	23.3131	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Rooted	Subtracted	Low confidence	48.9847	25.6716	23.3131	
2	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Measured	Subtracted	High confidence	41482.5	8126	33356.5	
2	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	Subtracted	High confidence	215	107	322	
2	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Ranked	Divided	Low confidence	223	1.47982	330	
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]	Ranked	Divided	High confidence	15	1.86667	28	
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]	Squared	Subtracted	High confidence	407289	143938	263351	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	Divided	High confidence	450.5	5.31521	2394.5	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Squared	Divided	High confidence	48.0356	28.2513	1357.07	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Rooted	Divided	High confidence	21.225	2.30547	48.9336	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Rooted	Subtracted	High confidence	21.225	27.7086	48.9336	
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Ranked	Divided	Low confidence	223	1.47982	330	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Measured	Divided	Low confidence	2399.5	4.4149	543.5	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Ranked	Subtracted	Low confidence	223	107	330	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Squared	Divided	Low confidence	1362.75	19.4914	69.9153	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Rooted	Divided	Low confidence	48.9847	2.10117	23.3131	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Rooted	Subtracted	Low confidence	48.9847	25.6716	23.3131	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Ranked	Divided	High confidence	15	1.86667	28	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Squared	Subtracted	High confidence	407289	143938	263351	
3	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Measured	Subtracted	High confidence	41482.5	8126	33356.5	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	Divided	High confidence	2597.5	3.71868	698.5	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Squared	Divided	High confidence	1596.92	13.8285	115.48	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	Divided	High confidence	50.9657	1.92839	26.4292	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	Subtracted	High confidence	50.9657	24.5365	26.4292	
3	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	Subtracted	Low confidence	21185	7307	28492	
3	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	Subtracted	High confidence	337	105	232	
3	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Squared	Subtracted	Low confidence	333506	141539	475045	
4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Measured	Subtracted	Low confidence	36474.3	7035.1	43509.4	
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Ranked	Divided	Low confidence	223	1.47982	330	

Legend:
- Rank is the rank after comparing the two networks
- 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/