MK5 Microarray Data

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

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Showing element 2351 to 2400 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
2351	synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	214.223	213.289	1.00438
2352	copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656]	215.088	214.155	1.00436
2353	electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	182.232	183.027
2354	copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670]	215.078	214.148	1.00434
2355	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	217.232	218.162	1.00428
2356	importin 4. [refseq;acc:nm_024658]	220.921	221.863	1.00426
2357	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	198.181	197.346	1.00423
2358	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
2359	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [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). [swissprot;acc:p09104]	207.186	208.046
2361	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
2362	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]	207.178	208.037
2363	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]	207.186	208.046
2364	transaldolase (ec 2.2.1.2). [swissprot;acc:p37837]	212.816	213.697	1.00414
2365	glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2]	208.958	209.82	1.00413
2366	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [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). [swissprot;acc:o00231]	217.589	218.475
2368	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]	218.555	219.434	1.00402
2369	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]
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). [swissprot;acc:q9y5k5]
2371	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
2372	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [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). [swissprot;acc:q15797]
2374	cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
2375	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]
2376	histone deacetylase 11 (hd11). [swissprot;acc:q96db2]
2377	ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9]
2378	ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
2379	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232]
2380	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837]
2381	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]
2382	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717]
2383	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757]
2384	dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [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). [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). [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). [swissprot;acc:p28074]	211.301	210.475	1.00392
2388	ring finger protein 20. [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. [refseq;acc:nm_014771]
2390	puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [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). [swissprot;acc:p09960]
2392	dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]
2393	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	182.266	182.962	1.00382
2394	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	221.662	220.826	1.00379
2395	26s protease regulatory subunit 7 (mss1 protein). [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). [swissprot;acc:p29312]	220.683	221.51	1.00375
2397	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	210.157	210.945
2398	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]	182.395	183.079
2399	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [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). [swissprot;acc:p23284]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.