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 Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 32 to 81 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
8	hbs1-like. [source:refseq;acc:nm_006620]	Ranked	215	322	1.49767	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Measured	398.5	1281.5	3.21581	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Squared	37.5863	388.696	10.3414	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Rooted	19.9625	35.798	1.79326	
9	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Ranked	212	309	1.45755	
10	protein x 0004. [source:refseq;acc:nm_016301]	Ranked	212	309	1.45755	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Measured	398.5	1281.5	3.21581	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Squared	37.5863	388.696	10.3414	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Rooted	19.9625	35.798	1.79326	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Measured	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Squared	37.5863	388.696	10.3414	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Rooted	19.9625	35.798	1.79326	
11	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	Ranked	337	232	1.45259	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Measured	398.5	1281.5	3.21581	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Squared	37.5863	388.696	10.3414	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Rooted	19.9625	35.798	1.79326	
12	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	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Measured	398.5	1281.5	3.21581	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Squared	37.5863	388.696	10.3414	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Rooted	19.9625	35.798	1.79326	
13	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Ranked	288.754	212.554	1.3585	
14	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Ranked	56.6768	75.3531	1.32952	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Measured	398.5	1281.5	3.21581	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Squared	37.5863	388.696	10.3414	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Rooted	19.9625	35.798	1.79326	
15	gbp protein isoform a. [source:refseq;acc:nm_017870]	Rooted	23.9771	42.4773	1.77158	
15	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Ranked	56.7244	75.3948	1.32914	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Measured	2671	871	3.06659	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Squared	1688.58	179.56	9.40399	
16	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Ranked	56.7252	75.3954	1.32913	
16	protein x 0004. [source:refseq;acc:nm_016301]	Measured	2671	871	3.06659	
16	protein x 0004. [source:refseq;acc:nm_016301]	Squared	1688.58	179.56	9.40399	
16	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	Rooted	51.6817	29.5127	1.75117	
17	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Ranked	56.7841	75.447	1.32866	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Measured	460	1365	2.96739	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Squared	50.0828	441	8.80542	
17	protein x 0004. [source:refseq;acc:nm_016301]	Rooted	51.6817	29.5127	1.75117	
18	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Ranked	185.678	245.247	1.32082	
18	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Rooted	21.4476	36.9459	1.72261	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Measured	677.5	1865.5	2.75351	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Squared	108.641	823.69	7.58176	
19	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Ranked	185.678	245.247	1.32082	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Measured	677.5	1865.5	2.75351	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Squared	108.641	823.69	7.58176	
19	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	Rooted	25.6987	43.561	1.69507	
20	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Ranked	185.678	245.247	1.32082	
20	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	Rooted	40.3337	24.2744	1.66157	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Measured	677.5	1865.5	2.75351	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Squared	108.641	823.69	7.58176	
21	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Measured	677.5	1865.5	2.75351	

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/