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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 3228 in total

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

Rank	green	red	network_comparison	description	
1	2394.5	450.5	5.31521	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	
2	2394.5	450.5	5.31521	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	
3	698.5	2597.5	3.71868	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	
4	698.5	2597.5	3.71868	hbs1-like. [source:refseq;acc:nm_006620]	
5	339.5	1153.5	3.39764	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	
6	339.5	1153.5	3.39764	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	
7	339.5	1153.5	3.39764	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]	
8	339.5	1153.5	3.39764	db83 protein. [source:swissprot;acc:p57088]	
9	1281.5	398.5	3.21581	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	
10	1281.5	398.5	3.21581	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	
11	1281.5	398.5	3.21581	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	
12	1281.5	398.5	3.21581	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	
13	1281.5	398.5	3.21581	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	
14	1281.5	398.5	3.21581	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	
15	871	2671	3.06659	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	
16	871	2671	3.06659	protein x 0004. [source:refseq;acc:nm_016301]	
17	1365	460	2.96739	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	
18	1865.5	677.5	2.75351	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	
19	1865.5	677.5	2.75351	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	
20	1865.5	677.5	2.75351	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	
21	1865.5	677.5	2.75351	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]	
22	1865.5	677.5	2.75351	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]	
23	1894.39	699.76	2.7072	gbp protein isoform a. [source:refseq;acc:nm_017870]	
24	2108.52	950.561	2.21818	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	
25	892.67	1833.01	2.0534	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	
26	892.67	1833.01	2.0534	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [source:swissprot;acc:q9ubi6]	
27	895.134	1834.33	2.04922	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [source:swissprot;acc:p50150]	
28	895.194	1834.36	2.04912	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [source:swissprot;acc:p29798]	
29	895.507	1834.52	2.04858	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [source:swissprot;acc:q9uk08]	
30	895.633	1834.59	2.04837	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [source:swissprot;acc:p30670]	
31	895.697	1834.63	2.04827	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	
32	895.893	1834.73	2.04793	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	
33	896.972	1835.3	2.04611	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	
34	907.546	1836.71	2.02382	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [source:swissprot;acc:p29992]	
35	907.564	1836.71	2.02378	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	
36	907.741	1836.76	2.02344	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [source:swissprot;acc:p19086]	
37	907.763	1836.76	2.02339	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [source:swissprot;acc:p11488]	
38	907.774	1836.76	2.02337	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [source:swissprot;acc:p19087]	
39	907.903	1836.8	2.02312	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04899]	
40	907.978	1836.81	2.02297	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [source:swissprot;acc:p04898]	
41	907.978	1836.81	2.02297	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [source:swissprot;acc:p08754]	
42	958.237	1857.32	1.93827	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	
43	1027.36	1881.02	1.83093	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	
44	1057.39	1931.34	1.82652	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	
45	1056.02	1926.69	1.82448	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	
46	1390.33	779.167	1.78438	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	
47	1390.33	779.167	1.78438	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	
48	1390.33	779.167	1.78438	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	
49	1390.33	779.167	1.78438	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	
50	1390.33	779.167	1.78438	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	

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/