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.

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Filtered	1
Interaction Map	High confidence

Rank	description	Network Comparison Type	Value Type	green	red	network_comparison	
1	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	Ranked	322	215	107	
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	Measured	33356.5	41482.5	8126	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Divided	Ranked	24	10	2.4	
1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	Squared	322755	468498	145743	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	Measured	2394.5	450.5	5.31521	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	Squared	1357.07	48.0356	28.2513	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Divided	Rooted	48.9336	21.225	2.30547	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	Rooted	48.9336	21.225	27.7086	
2	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	Measured	33356.5	41482.5	8126	
2	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	Ranked	322	215	107	
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	Ranked	28	15	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	Squared	263351	407289	143938	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	Measured	2394.5	450.5	5.31521	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	Squared	1357.07	48.0356	28.2513	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Divided	Rooted	48.9336	21.225	2.30547	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	Rooted	48.9336	21.225	27.7086	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Divided	Ranked	28	15	1.86667	
3	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Subtracted	Squared	263351	407289	143938	
3	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	Measured	33356.5	41482.5	8126	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	Measured	698.5	2597.5	3.71868	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	Squared	115.48	1596.92	13.8285	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	Rooted	26.4292	50.9657	1.92839	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Subtracted	Rooted	26.4292	50.9657	24.5365	
3	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Subtracted	Ranked	232	337	105	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Divided	Ranked	28	15	1.86667	
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Subtracted	Squared	263351	407289	143938	
4	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	Measured	33356.5	41482.5	8126	
4	hbs1-like. [source:refseq;acc:nm_006620]	Divided	Measured	698.5	2597.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	Divided	Squared	115.48	1596.92	13.8285	
4	hbs1-like. [source:refseq;acc:nm_006620]	Divided	Rooted	26.4292	50.9657	1.92839	
4	hbs1-like. [source:refseq;acc:nm_006620]	Subtracted	Rooted	26.4292	50.9657	24.5365	
4	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Subtracted	Ranked	232	337	105	
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	Rooted	168.796	145.551	23.245	
5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	Measured	33356.5	41482.5	8126	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Divided	Ranked	28	15	1.86667	
5	cytohesin 4. [source:swissprot;acc:q9uia0]	Subtracted	Squared	263351	407289	143938	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	Measured	339.5	1153.5	3.39764	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	Squared	27.2805	314.926	11.544	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Divided	Rooted	18.4255	33.9632	1.84327	
5	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Subtracted	Ranked	309	212	97	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Divided	Ranked	28	15	1.86667	
6	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Subtracted	Squared	263351	407289	143938	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	Measured	339.5	1153.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	Squared	27.2805	314.926	11.544	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Divided	Rooted	18.4255	33.9632	1.84327	
6	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Subtracted	Rooted	168.796	145.551	23.245	
6	protein x 0004. [source:refseq;acc:nm_016301]	Subtracted	Ranked	309	212	97	
6	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Subtracted	Measured	36927.5	44490.5	7563	
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Subtracted	Measured	28492	21185	7307	
7	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Divided	Ranked	322	215	1.49767	

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/