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 Value Type description 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	Value Type	description	Interaction Map	red	green	network_comparison	
1	Measured	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	2399.5	543.5	4.4149	
1	Measured	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	450.5	2394.5	5.31521	
1	Ranked	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	16	32	2	
1	Ranked	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	High confidence	10	24	2.4	
1	Squared	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	1362.75	69.9153	19.4914	
1	Squared	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	48.0356	1357.07	28.2513	
1	Rooted	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	48.9847	23.3131	2.10117	
1	Rooted	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	21.225	48.9336	2.30547	
2	Measured	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	2399.5	543.5	4.4149	
2	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	450.5	2394.5	5.31521	
2	Ranked	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	223	330	1.47982	
2	Ranked	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]	High confidence	15	28	1.86667	
2	Squared	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	1362.75	69.9153	19.4914	
2	Squared	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	48.0356	1357.07	28.2513	
2	Rooted	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	48.9847	23.3131	2.10117	
2	Rooted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	21.225	48.9336	2.30547	
3	Measured	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	2399.5	543.5	4.4149	
3	Measured	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	2597.5	698.5	3.71868	
3	Ranked	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	223	330	1.47982	
3	Ranked	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	High confidence	15	28	1.86667	
3	Squared	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	1362.75	69.9153	19.4914	
3	Squared	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	1596.92	115.48	13.8285	
3	Rooted	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	48.9847	23.3131	2.10117	
3	Rooted	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	50.9657	26.4292	1.92839	
4	Measured	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	2597.5	698.5	3.71868	
4	Measured	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	2399.5	543.5	4.4149	
4	Ranked	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	223	330	1.47982	
4	Ranked	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	15	28	1.86667	
4	Squared	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	1596.92	115.48	13.8285	
4	Squared	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	1362.75	69.9153	19.4914	
4	Rooted	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	50.9657	26.4292	1.92839	
4	Rooted	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	48.9847	23.3131	2.10117	
5	Measured	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	1153.5	339.5	3.39764	
5	Measured	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	736.5	2113.5	2.86965	
5	Ranked	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	15	28	1.86667	
5	Ranked	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	223	330	1.47982	
5	Squared	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	314.926	27.2805	11.544	
5	Squared	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	128.386	1057.25	8.23493	
5	Rooted	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	33.9632	18.4255	1.84327	
5	Rooted	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	27.1385	45.9728	1.69401	
6	Measured	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	1153.5	339.5	3.39764	
6	Measured	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	736.5	2113.5	2.86965	
6	Ranked	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	High confidence	15	28	1.86667	
6	Ranked	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	318	240	1.325	
6	Squared	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	314.926	27.2805	11.544	
6	Squared	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	128.386	1057.25	8.23493	
6	Rooted	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	33.9632	18.4255	1.84327	
6	Rooted	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	27.1385	45.9728	1.69401	
7	Measured	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	736.5	2113.5	2.86965	
7	Measured	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]	High confidence	1153.5	339.5	3.39764	

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/