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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Value Type Interaction Map description Rank Network Comparison Type Gene red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 732 to 781 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	1239	5654.53	6132.76	1.08457	
db83 protein. [source:swissprot;acc:p57088]	8	1153.5	339.5	3.39764	
dc11 protein. [source:refseq;acc:nm_020186]	1908	6858.84	7287.27	1.06246	
dc12 protein. [source:refseq;acc:nm_020187]	2774	0.00001	0.00001	1	
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [source:refseq;acc:nm_022779]	431	3849.94	4431.36	1.15102	
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	777	5874.74	6533.34	1.11211	
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	2284	5783.73	6048.91	1.04585	
dead-box protein 4 (vasa homolog). [source:swissprot;acc:q9nqi0]	990	5147.9	5641.25	1.09584	
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	2033	6101.12	6449.87	1.05716	
dead-box protein. [source:refseq;acc:nm_018665]	1064	5719.01	6248.6	1.0926	
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	2497	7002.3	7192.25	1.02713	
defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	2391	6327.14	6579.38	1.03987	
deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [source:swissprot;acc:o75398]	2584	4180.32	4253.46	1.0175	
dehydrodolichyl diphosphate synthase. [source:refseq;acc:nm_024887]	1280	6350.81	6874.88	1.08252	
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [source:swissprot;acc:p54886]	1488	5573.64	5991.58	1.07499	
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [source:swissprot;acc:o76062]	2309	6960.96	7273.7	1.04493	
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [source:swissprot;acc:p13716]	1158	5489.18	5972.09	1.08797	
delta-interacting protein a (hepatitis delta antigen interacting protein a). [source:swissprot;acc:q15834]	1410	6274.62	6760.78	1.07748	
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	738	5768.32	6434.78	1.11554	
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	1019	5791.82	6340.86	1.0948	
deltex 2. [source:refseq;acc:nm_020892]	54	1618.84	2651.88	1.63814	
deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	55	1629.21	2662.12	1.63399	
dendritic cell protein. [source:refseq;acc:nm_006360]	715	6593.17	7364.55	1.117	
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	1589	3600.99	3360.33	1.07162	
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [source:swissprot;acc:p32321]	2148	4644.58	4892.06	1.05328	
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [source:swissprot;acc:p49366]	1493	6146.36	6606.21	1.07482	
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	324	28136.5	33457.6	1.18912	
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	567	10264.9	9043.51	1.13506	
destrin (actin-depolymerizing factor) (adf). [source:swissprot;acc:p18282]	1948	6230.21	6608.64	1.06074	
developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	2762	0.00001	0.00001	1	
developmentally regulated gtp-binding protein 2 (drg 2). [source:swissprot;acc:p55039]	3092	0.00001	0.00001	1	
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	17	460	1365	2.96739	
dgcr8 protein (digeorge syndrome critical region 8). [source:swissprot;acc:q8wyq5]	3006	0.00001	0.00001	1	
di-ras2. [source:refseq;acc:nm_017594]	706	6912.08	7734.39	1.11897	
dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	1803	4980.54	5307.81	1.06571	
dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [source:swissprot;acc:p10515]	2464	6291.2	6486.07	1.03098	
dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [source:swissprot;acc:p09622]	2600	6185	6283.8	1.01597	
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [source:swissprot;acc:p36957]	2535	6452.33	6603.94	1.0235	
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	830	5745.61	6354.75	1.10602	
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	714	5222.71	5834.57	1.11715	
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [source:refseq;acc:nm_014475]	1629	6158.32	6590.99	1.07026	
dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [source:swissprot;acc:q01740]	975	5365.14	5884.43	1.09679	
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [source:swissprot;acc:q99518]	974	5365.06	5884.52	1.09682	
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	956	5364.77	5884.89	1.09695	
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [source:swissprot;acc:p31512]	976	5365.22	5884.32	1.09675	
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [source:swissprot;acc:p49326]	951	5364.3	5885.48	1.09716	
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	930	5638.65	6194.23	1.09853	
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	2669	4336.58	4310.3	1.0061	
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	927	5638.64	6194.22	1.09853	
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	2670	4336.62	4310.35	1.00609	

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/