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 2358 to 2407 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2358	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [source:swissprot;acc:q14318]	198.181	197.346	1.00423	
2359	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	207.196	208.056	1.00415	
2360	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [source:swissprot;acc:p09104]	207.186	208.046	1.00415	
2361	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [source:swissprot;acc:p13929]	207.186	208.046	1.00415	
2362	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	207.178	208.037	1.00415	
2363	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [source:swissprot;acc:p06733]	207.186	208.046	1.00415	
2364	transaldolase (ec 2.2.1.2). [source:swissprot;acc:p37837]	212.816	213.697	1.00414	
2365	glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	208.958	209.82	1.00413	
2366	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [source:swissprot;acc:p52758]	203.353	202.529	1.00407	
2367	26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [source:swissprot;acc:o00231]	217.589	218.475	1.00407	
2368	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [source:swissprot;acc:q99460]	218.555	219.434	1.00402	
2369	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [source:swissprot;acc:q16186]	218.555	219.434	1.00402	
2370	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [source:swissprot;acc:q9y5k5]	218.555	219.434	1.00402	
2371	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [source:swissprot;acc:o94763]	218.555	219.434	1.00402	
2372	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [source:swissprot;acc:q15796]	212.724	213.574	1.004	
2373	mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [source:swissprot;acc:q15797]	212.724	213.574	1.004	
2374	cop9 subunit 6 (mov34 homolog, 34 kd). [source:refseq;acc:nm_006833]	212.724	213.574	1.004	
2375	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [source:swissprot;acc:q92940]	212.724	213.574	1.004	
2376	histone deacetylase 11 (hd11). [source:swissprot;acc:q96db2]	212.724	213.574	1.004	
2377	ethanolamine kinase-like protein eki2 (flj10761). [source:swissprot;acc:q9nvf9]	212.724	213.574	1.004	
2378	ethanolamine kinase (ec 2.7.1.82) (eki). [source:swissprot;acc:q9hbu6]	212.724	213.574	1.004	
2379	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [source:refseq;acc:nm_020232]	212.724	213.574	1.004	
2380	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [source:refseq;acc:nm_006837]	212.724	213.574	1.004	
2381	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [source:swissprot;acc:o15198]	212.724	213.574	1.004	
2382	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [source:swissprot;acc:q99717]	212.724	213.574	1.004	
2383	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [source:swissprot;acc:q99757]	212.724	213.574	1.004	
2384	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [source:swissprot;acc:p52564]	210.57	209.737	1.00397	
2385	dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [source:swissprot;acc:p46734]	210.595	209.767	1.00395	
2386	nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [source:swissprot;acc:o96000]	213.82	212.983	1.00393	
2387	proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [source:swissprot;acc:p28074]	211.301	210.475	1.00392	
2388	ring finger protein 20. [source:refseq;acc:nm_019592]	224.414	225.289	1.0039	
2389	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [source:refseq;acc:nm_014771]	224.414	225.289	1.0039	
2390	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	214.966	215.799	1.00388	
2391	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	214.966	215.799	1.00388	
2392	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	214.966	215.799	1.00388	
2393	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	182.266	182.962	1.00382	
2394	n-acetyltransferase 5 (ec 2.3.1.-). [source:swissprot;acc:q9y6d2]	221.662	220.826	1.00379	
2395	26s protease regulatory subunit 7 (mss1 protein). [source:swissprot;acc:p35998]	218.192	219.014	1.00377	
2396	14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [source:swissprot;acc:p29312]	220.683	221.51	1.00375	
2397	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	210.157	210.945	1.00375	
2398	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	182.395	183.079	1.00375	
2399	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	182.4	183.083	1.00374	
2400	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	182.4	183.083	1.00374	
2401	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	182.4	183.083	1.00374	
2402	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	182.4	183.083	1.00374	
2403	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	182.4	183.083	1.00374	
2404	acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [source:swissprot;acc:q99424]	193.389	194.105	1.0037	
2405	thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [source:refseq;acc:nm_006472]	221.677	222.489	1.00366	
2406	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [source:refseq;acc:nm_005843]	182.563	183.232	1.00366	
2407	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [source:swissprot;acc:p49720]	214.234	213.456	1.00364	

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/