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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3228 in total

Network Comparison Type	Divided
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	450.5	2394.5	5.31521	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	450.5	2394.5	5.31521	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	2597.5	698.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	2597.5	698.5	3.71868	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	1153.5	339.5	3.39764	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	1153.5	339.5	3.39764	
7	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]	1153.5	339.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	1153.5	339.5	3.39764	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	398.5	1281.5	3.21581	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	398.5	1281.5	3.21581	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	398.5	1281.5	3.21581	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	398.5	1281.5	3.21581	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	398.5	1281.5	3.21581	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	2671	871	3.06659	
16	protein x 0004. [source:refseq;acc:nm_016301]	2671	871	3.06659	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	460	1365	2.96739	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	677.5	1865.5	2.75351	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	677.5	1865.5	2.75351	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	677.5	1865.5	2.75351	
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]	677.5	1865.5	2.75351	
22	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	677.5	1865.5	2.75351	
23	gbp protein isoform a. [source:refseq;acc:nm_017870]	699.76	1894.39	2.7072	
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	950.561	2108.52	2.21818	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	1833.01	892.67	2.0534	
26	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	1833.01	892.67	2.0534	
27	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	1834.33	895.134	2.04922	
28	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	1834.36	895.194	2.04912	
29	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	1834.52	895.507	2.04858	
30	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	1834.59	895.633	2.04837	
31	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	1834.63	895.697	2.04827	
32	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	1834.73	895.893	2.04793	
33	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	1835.3	896.972	2.04611	
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	1836.71	907.546	2.02382	
35	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	1836.71	907.564	2.02378	
36	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	1836.76	907.741	2.02344	
37	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	1836.76	907.763	2.02339	
38	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	1836.76	907.774	2.02337	
39	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	1836.8	907.903	2.02312	
40	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	1836.81	907.978	2.02297	
41	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	1836.81	907.978	2.02297	
42	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	1857.32	958.237	1.93827	
43	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	1881.02	1027.36	1.83093	
44	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	1931.34	1057.39	1.82652	
45	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	1926.69	1056.02	1.82448	
46	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	779.167	1390.33	1.78438	
47	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	779.167	1390.33	1.78438	
48	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	779.167	1390.33	1.78438	
49	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	779.167	1390.33	1.78438	
50	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	779.167	1390.33	1.78438	

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/