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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Value Type	red	green	network_comparison	
1	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Measured	450.5	2394.5	5.31521	
1	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Squared	48.0356	1357.07	28.2513	
1	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Rooted	21.225	48.9336	2.30547	
1	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	Ranked	10	24	2.4	
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	15	28	1.86667	
2	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	450.5	2394.5	5.31521	
2	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Squared	48.0356	1357.07	28.2513	
2	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Rooted	21.225	48.9336	2.30547	
3	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	2597.5	698.5	3.71868	
3	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Squared	1596.92	115.48	13.8285	
3	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Rooted	50.9657	26.4292	1.92839	
3	PSCD1	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Ranked	15	28	1.86667	
4	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Measured	2597.5	698.5	3.71868	
4	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Squared	1596.92	115.48	13.8285	
4	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Rooted	50.9657	26.4292	1.92839	
4	PSCD2	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	Ranked	15	28	1.86667	
5	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Measured	1153.5	339.5	3.39764	
5	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Squared	314.926	27.2805	11.544	
5	JPH3	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	Rooted	33.9632	18.4255	1.84327	
5	PSCD4	cytohesin 4. [source:swissprot;acc:q9uia0]	Ranked	15	28	1.86667	
6	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Measured	1153.5	339.5	3.39764	
6	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Squared	314.926	27.2805	11.544	
6	JPH2	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	Rooted	33.9632	18.4255	1.84327	
6	PSCD3	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	Ranked	15	28	1.86667	
7	HLX	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Ranked	215	322	1.49767	
7	SMPD2	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]	Measured	1153.5	339.5	3.39764	
7	SMPD2	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]	Squared	314.926	27.2805	11.544	
7	SMPD2	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]	Rooted	33.9632	18.4255	1.84327	
8	HBS1L	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	215	322	1.49767	
8	TMEM33	db83 protein. [source:swissprot;acc:p57088]	Measured	1153.5	339.5	3.39764	
8	TMEM33	db83 protein. [source:swissprot;acc:p57088]	Squared	314.926	27.2805	11.544	
8	TMEM33	db83 protein. [source:swissprot;acc:p57088]	Rooted	33.9632	18.4255	1.84327	
9	TOB2	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	398.5	1281.5	3.21581	
9	TOB2	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	37.5863	388.696	10.3414	
9	TOB2	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	19.9625	35.798	1.79326	
9	XAB1	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	212	309	1.45755	
10	ATPBD1C	protein x 0004. [source:refseq;acc:nm_016301]	Ranked	212	309	1.45755	
10	TOB1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Measured	398.5	1281.5	3.21581	
10	TOB1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Squared	37.5863	388.696	10.3414	
10	TOB1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Rooted	19.9625	35.798	1.79326	
11	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Measured	398.5	1281.5	3.21581	
11	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Squared	37.5863	388.696	10.3414	
11	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	19.9625	35.798	1.79326	
11	RINT1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	337	232	1.45259	
12	CPEB4	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Measured	398.5	1281.5	3.21581	
12	CPEB4	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Squared	37.5863	388.696	10.3414	
12	CPEB4	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Rooted	19.9625	35.798	1.79326	
12	RHOBTB2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Ranked	337	232	1.45259	
13	CPEB3	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Measured	398.5	1281.5	3.21581	
13	CPEB3	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Squared	37.5863	388.696	10.3414	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/