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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 33156 in total

Filtered	1
Network Comparison Type	Divided

Rank	description	Value Type	Interaction Map	red	network_comparison	green	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Ranked	Low confidence	16	2	32	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Measured	Low confidence	2399.5	4.4149	543.5	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Squared	Low confidence	1362.75	19.4914	69.9153	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Rooted	Low confidence	48.9847	2.10117	23.3131	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Ranked	High confidence	10	2.4	24	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	High confidence	450.5	5.31521	2394.5	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Squared	High confidence	48.0356	28.2513	1357.07	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	High confidence	21.225	2.30547	48.9336	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Measured	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]	Squared	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	Low confidence	48.9847	2.10117	23.3131	
2	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Ranked	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	High confidence	15	1.86667	28	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	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	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	High confidence	21.225	2.30547	48.9336	
3	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Ranked	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	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]	Squared	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	Low confidence	48.9847	2.10117	23.3131	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Ranked	High confidence	15	1.86667	28	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	High confidence	2597.5	3.71868	698.5	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Squared	High confidence	1596.92	13.8285	115.48	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	High confidence	50.9657	1.92839	26.4292	
4	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Ranked	Low confidence	223	1.47982	330	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	High confidence	15	1.86667	28	
4	hbs1-like. [source:refseq;acc:nm_006620]	Measured	High confidence	2597.5	3.71868	698.5	
4	hbs1-like. [source:refseq;acc:nm_006620]	Squared	High confidence	1596.92	13.8285	115.48	
4	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	High confidence	50.9657	1.92839	26.4292	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Measured	Low confidence	2399.5	4.4149	543.5	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Squared	Low confidence	1362.75	19.4914	69.9153	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Rooted	Low confidence	48.9847	2.10117	23.3131	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	High confidence	15	1.86667	28	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	High confidence	1153.5	3.39764	339.5	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	High confidence	314.926	11.544	27.2805	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	High confidence	33.9632	1.84327	18.4255	
5	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Ranked	Low confidence	223	1.47982	330	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Measured	Low confidence	736.5	2.86965	2113.5	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Squared	Low confidence	128.386	8.23493	1057.25	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Rooted	Low confidence	27.1385	1.69401	45.9728	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Ranked	High confidence	15	1.86667	28	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	High confidence	1153.5	3.39764	339.5	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	High confidence	314.926	11.544	27.2805	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	High confidence	33.9632	1.84327	18.4255	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Measured	Low confidence	736.5	2.86965	2113.5	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Squared	Low confidence	128.386	8.23493	1057.25	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Rooted	Low confidence	27.1385	1.69401	45.9728	
6	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Ranked	Low confidence	318	1.325	240	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	High confidence	215	1.49767	322	
7	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Ranked	Low confidence	318	1.325	240	

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/