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 1 to 50 of 8289 in total

Value Type	Measured
Network Comparison Type	Divided
Filtered	1

Rank	description	Interaction Map	red	green	network_comparison	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	2399.5	543.5	4.4149	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	450.5	2394.5	5.31521	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	2399.5	543.5	4.4149	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	450.5	2394.5	5.31521	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	2399.5	543.5	4.4149	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	2597.5	698.5	3.71868	
4	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	2597.5	698.5	3.71868	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	2399.5	543.5	4.4149	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	1153.5	339.5	3.39764	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	736.5	2113.5	2.86965	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	1153.5	339.5	3.39764	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	736.5	2113.5	2.86965	
7	oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [source:swissprot;acc:q9bzf2]	Low confidence	736.5	2113.5	2.86965	
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]	High confidence	1153.5	339.5	3.39764	
8	db83 protein. [source:swissprot;acc:p57088]	High confidence	1153.5	339.5	3.39764	
8	phosphatidylinositol-glycan biosynthesis, class f protein (pig-f). [source:swissprot;acc:q07326]	Low confidence	3278	5058.5	1.54317	
9	n33 protein. [source:swissprot;acc:q13454]	Low confidence	3278	5058.5	1.54317	
9	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	High confidence	398.5	1281.5	3.21581	
10	implantation-associated protein. [source:refseq;acc:nm_032121]	Low confidence	3278	5058.5	1.54317	
10	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	High confidence	398.5	1281.5	3.21581	
11	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	High confidence	398.5	1281.5	3.21581	
11	thyroid receptor interacting protein 8 (trip-8) (fragment). [source:swissprot;acc:q15652]	Low confidence	1917.64	2950.5	1.53861	
12	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	High confidence	398.5	1281.5	3.21581	
12	gbp protein isoform a. [source:refseq;acc:nm_017870]	Low confidence	1921.96	2954.24	1.5371	
13	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	High confidence	398.5	1281.5	3.21581	
13	jumonji domain containing 1; zinc finger protein; testis-specific protein a. [source:refseq;acc:nm_018433]	Low confidence	1927.68	2959.19	1.5351	
14	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	High confidence	398.5	1281.5	3.21581	
14	trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [source:swissprot;acc:p35030]	Low confidence	1972.65	2998.1	1.51983	
15	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [source:swissprot;acc:p07477]	Low confidence	1983.91	3007.85	1.51612	
15	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [source:refseq;acc:nm_007266]	High confidence	2671	871	3.06659	
16	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	21185	28492	1.34491	
16	protein x 0004. [source:refseq;acc:nm_016301]	High confidence	2671	871	3.06659	
17	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	High confidence	460	1365	2.96739	
17	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	21185	28492	1.34491	
18	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Low confidence	5492.04	7251	1.32027	
18	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	High confidence	677.5	1865.5	2.75351	
19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	Low confidence	3032.56	3915.4	1.29112	
19	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	High confidence	677.5	1865.5	2.75351	
20	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	High confidence	677.5	1865.5	2.75351	
20	retinoblastoma-associated factor 600. [source:refseq;acc:nm_020765]	Low confidence	7256.71	9368.87	1.29106	
21	cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [source:swissprot;acc:q02318]	Low confidence	3035.43	3917.88	1.29072	
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]	High confidence	677.5	1865.5	2.75351	
22	cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [source:swissprot;acc:q07973]	Low confidence	3126.88	3997.02	1.27828	
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]	High confidence	677.5	1865.5	2.75351	
23	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	40899	32028.5	1.27696	
23	gbp protein isoform a. [source:refseq;acc:nm_017870]	High confidence	699.76	1894.39	2.7072	
24	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Low confidence	5720.25	4577.5	1.24965	
24	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [source:refseq;acc:nm_003690]	High confidence	950.561	2108.52	2.21818	
25	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [source:swissprot;acc:o60262]	High confidence	1833.01	892.67	2.0534	
25	histidine triad nucleotide-binding protein 1 (adenosine 5'- monophosphoramidase) (protein kinase c inhibitor 1) (protein kinase c- interacting protein 1) (pkci-1). [source:swissprot;acc:p49773]	Low confidence	5847.46	4691.96	1.24627	

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/