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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 66312 in total

Filtered	1

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

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/