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 Network Comparison Type Value Type description Filtered Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 2277 to 2326 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Filtered	1
Interaction Map	High confidence

Rank	description	network_comparison	green	red	
2277	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	1.00538	190.909	191.936	
2278	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [source:swissprot;acc:o60315]	1.00538	190.909	191.936	
2279	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [source:swissprot;acc:p37275]	1.00538	190.909	191.936	
2280	proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [source:swissprot;acc:o14818]	1.00537	211.657	212.793	
2281	splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [source:refseq;acc:nm_016333]	1.00536	218.482	219.652	
2282	splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [source:swissprot;acc:q01081]	1.00536	218.482	219.652	
2283	proteasome subunit alpha type 7-like (ec 3.4.25.1). [source:swissprot;acc:q8taa3]	1.00536	211.676	212.81	
2284	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [source:refseq;acc:nm_007372]	1.00536	218.482	219.652	
2285	splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [source:swissprot;acc:p26368]	1.00536	218.482	219.652	
2286	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]	1.00535	215.456	216.608	
2287	phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [source:swissprot;acc:q13393]	1.00535	205.376	206.475	
2288	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]	1.00533	215.458	216.607	
2289	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]	1.00531	215.46	216.605	
2290	myo-inositol 1-phosphate synthase a1. [source:refseq;acc:nm_016368]	1.00527	201.213	200.158	
2291	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	1.00527	201.213	200.158	
2292	ubiquitin-like protein gdx (ubiquitin-like protein 4). [source:swissprot;acc:p11441]	1.00527	201.213	200.158	
2293	large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [source:swissprot;acc:p46379]	1.00527	201.213	200.158	
2294	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	1.00527	163.187	162.331	
2295	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [source:swissprot;acc:q13625]	1.00523	163.712	162.86	
2296	phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [source:swissprot;acc:o14939]	1.00521	205.38	206.451	
2297	epsin 3. [source:refseq;acc:nm_017957]	1.00518	219.284	218.153	
2298	ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [source:swissprot;acc:q93068]	1.00511	216.339	215.239	
2299	udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [source:swissprot;acc:o60701]	1.00511	216.339	215.239	
2300	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1.00511	192.541	191.563	
2301	nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [source:refseq;acc:nm_178177]	1.00509	218.498	217.392	
2302	hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [source:swissprot;acc:p54868]	1.00509	192.542	191.567	
2303	3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [source:swissprot;acc:p04035]	1.00509	192.542	191.567	
2304	hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [source:swissprot;acc:q01581]	1.00509	192.542	191.567	
2305	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]	1.00509	218.498	217.392	
2306	acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [source:swissprot;acc:p24752]	1.00508	192.544	191.571	
2307	camp-dependent protein kinase type ii-alpha regulatory chain. [source:swissprot;acc:p13861]	1.00507	214.467	215.554	
2308	protein kinase pkx1 (ec 2.7.1.-). [source:swissprot;acc:p51817]	1.00505	214.459	215.543	
2309	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [source:swissprot;acc:p22612]	1.00505	214.459	215.542	
2310	ubiquitin. [source:swissprot;acc:p02248]	1.00505	215.529	216.617	
2311	camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [source:swissprot;acc:p22694]	1.00505	214.459	215.542	
2312	camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [source:swissprot;acc:p17612]	1.00505	214.459	215.542	
2313	camp-dependent protein kinase type ii-beta regulatory chain. [source:swissprot;acc:p31323]	1.00504	214.449	215.529	
2314	ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [source:swissprot;acc:p51669]	1.00496	195.708	194.743	
2315	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:o00763]	1.00494	195.787	194.825	
2316	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	1.00493	218.311	217.241	
2317	serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [source:swissprot;acc:o00743]	1.00493	195.794	194.834	
2318	sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	1.00493	195.794	194.834	
2319	acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:q13085]	1.00492	195.8	194.842	
2320	rad54-like protein; rad54 homolog. [source:refseq;acc:nm_003579]	1.00492	218.218	219.292	
2321	tetratricopeptide repeat protein 4 (my044 protein). [source:swissprot;acc:o95801]	1.00485	202.925	203.909	
2322	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [source:refseq;acc:nm_014317]	1.00476	234.905	236.023	
2323	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [source:swissprot;acc:o43776]	1.00476	193.691	192.773	
2324	proteasome subunit beta type 1 (ec 3.4.25.1) (proteasome component c5) (macropain subunit c5) (multicatalytic endopeptidase complex subunit c5) (proteasome gamma chain). [source:swissprot;acc:p20618]	1.00474	211.129	212.129	
2325	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [source:swissprot;acc:q96dp5]	1.00473	220.685	221.728	
2326	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [source:swissprot;acc:p45985]	1.00468	219.05	220.076	

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/