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 2375 to 2424 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
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	
2408	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [source:sptrembl;acc:q9uge0]	194.407	193.706	1.00362	
2409	lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [source:swissprot;acc:q04760]	194.407	193.706	1.00362	
2410	lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [source:refseq;acc:nm_006330]	194.407	193.706	1.00362	
2411	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [source:swissprot;acc:p30039]	194.407	193.706	1.00362	
2412	lysophospholipase ii; acyl-protein thioesterase. [source:refseq;acc:nm_007260]	194.407	193.706	1.00362	
2413	serpin b12. [source:swissprot;acc:q96p63]	218.2	218.984	1.00359	
2414	megsin (tp55) (serpin b7). [source:swissprot;acc:o75635]	218.2	218.984	1.00359	
2415	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	218.2	218.984	1.00359	
2416	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [source:swissprot;acc:p55055]	218.2	218.984	1.00359	
2417	upf0183 protein. [source:swissprot;acc:q9bsu1]	218.2	218.984	1.00359	
2418	antithrombin-iii precursor (atiii) (pro0309). [source:swissprot;acc:p01008]	218.2	218.984	1.00359	
2419	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q14232]	218.2	218.984	1.00359	
2420	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [source:swissprot;acc:p29508]	218.2	218.984	1.00359	
2421	apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [source:refseq;acc:nm_032797]	210.205	209.454	1.00359	
2422	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [source:swissprot;acc:q13133]	218.2	218.984	1.00359	
2423	histone deacetylase 5 (hd5) (antigen ny-co-9). [source:swissprot;acc:q9uql6]	220.682	221.471	1.00358	
2424	histone deacetylase 4 (hd4). [source:swissprot;acc:p56524]	220.682	221.472	1.00358	

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/