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.

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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 33156 in total

Network Comparison Type	Divided
Filtered	1

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

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/