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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 25824 in total

Filtered	1
Interaction Map	High confidence

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