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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red 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	green	red	network_comparison	
2358	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [source:swissprot;acc:q14318]	197.346	198.181	1.00423	
2359	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [source:swissprot;acc:p07205]	208.056	207.196	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]	208.046	207.186	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]	208.046	207.186	1.00415	
2362	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [source:swissprot;acc:p00558]	208.037	207.178	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]	208.046	207.186	1.00415	
2364	transaldolase (ec 2.2.1.2). [source:swissprot;acc:p37837]	213.697	212.816	1.00414	
2365	glutamate carboxypeptidase-like protein 2 precursor. [source:swissprot;acc:q96kn2]	209.82	208.958	1.00413	
2366	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [source:swissprot;acc:p52758]	202.529	203.353	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]	218.475	217.589	1.00407	
2368	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [source:swissprot;acc:q99460]	219.434	218.555	1.00402	
2369	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [source:swissprot;acc:q16186]	219.434	218.555	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]	219.434	218.555	1.00402	
2371	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [source:swissprot;acc:o94763]	219.434	218.555	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]	213.574	212.724	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]	213.574	212.724	1.004	
2374	cop9 subunit 6 (mov34 homolog, 34 kd). [source:refseq;acc:nm_006833]	213.574	212.724	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]	213.574	212.724	1.004	
2376	histone deacetylase 11 (hd11). [source:swissprot;acc:q96db2]	213.574	212.724	1.004	
2377	ethanolamine kinase-like protein eki2 (flj10761). [source:swissprot;acc:q9nvf9]	213.574	212.724	1.004	
2378	ethanolamine kinase (ec 2.7.1.82) (eki). [source:swissprot;acc:q9hbu6]	213.574	212.724	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]	213.574	212.724	1.004	
2380	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [source:refseq;acc:nm_006837]	213.574	212.724	1.004	
2381	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [source:swissprot;acc:o15198]	213.574	212.724	1.004	
2382	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [source:swissprot;acc:q99717]	213.574	212.724	1.004	
2383	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [source:swissprot;acc:q99757]	213.574	212.724	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]	209.737	210.57	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]	209.767	210.595	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]	212.983	213.82	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]	210.475	211.301	1.00392	
2388	ring finger protein 20. [source:refseq;acc:nm_019592]	225.289	224.414	1.0039	
2389	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [source:refseq;acc:nm_014771]	225.289	224.414	1.0039	
2390	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [source:swissprot;acc:p55786]	215.799	214.966	1.00388	
2391	leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [source:swissprot;acc:p09960]	215.799	214.966	1.00388	
2392	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [source:swissprot;acc:q02127]	215.799	214.966	1.00388	
2393	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	182.962	182.266	1.00382	
2394	n-acetyltransferase 5 (ec 2.3.1.-). [source:swissprot;acc:q9y6d2]	220.826	221.662	1.00379	
2395	26s protease regulatory subunit 7 (mss1 protein). [source:swissprot;acc:p35998]	219.014	218.192	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]	221.51	220.683	1.00375	
2397	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	210.945	210.157	1.00375	
2398	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	183.079	182.395	1.00375	
2399	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	183.083	182.4	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]	183.083	182.4	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]	183.083	182.4	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]	183.083	182.4	1.00374	
2403	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	183.083	182.4	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]	194.105	193.389	1.0037	
2405	thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [source:refseq;acc:nm_006472]	222.489	221.677	1.00366	
2406	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [source:refseq;acc:nm_005843]	183.232	182.563	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]	213.456	214.234	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/