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

Results: HTML CSV LaTeX

Showing element 2313 to 2362 of 3228 in total

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

Rank	description	red	green	network_comparison
2313	disrupter of silencing 10. [refseq;acc:nm_020368]	6960.96	7273.7	1.04493
2314	very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	6960.99	7273.72
2315	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	6961.11	7273.85
2316	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	6960.74	7273.48
2317	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	6961.44	7274.17	1.04492
2318	ubiquitin. [swissprot;acc:p02248]	7484.98	7821.11	1.04491
2319	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	6362.48	6647.42	1.04478
2320	t54 protein. [swissprot;acc:q92917]
2321	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9]	3496.21	3652.28	1.04464
2322	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]	6773.67	7075.51	1.04456
2323	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]
2324	cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
2325	mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940]
2326	histone deacetylase 11 (hd11). [swissprot;acc:q96db2]
2327	ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9]
2328	ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6]
2329	hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232]
2330	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837]
2331	mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198]
2332	mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717]
2333	thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757]
2334	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	5123.89	5350.78	1.04428
2335	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
2336	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]
2337	cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
2338	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
2339	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]
2340	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1]	5607.81	5855.72	1.04421
2341	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792]	5606.66	5854.45	1.0442
2342	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	7007.72	7317.15	1.04416
2343	40s ribosomal protein s5. [swissprot;acc:p46782]	3672.17	3516.98	1.04413
2344	carboxypeptidase a5. [refseq;acc:nm_080385]	8353.97	8001.45	1.04406
2345	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
2346	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]
2347	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	6480.27	6765.81
2348	ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
2349	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	8353.97	8001.45
2350	stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]	6480.27	6765.81
2351	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	8353.97	8001.45
2352	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579]	8493.7	8135.59	1.04402
2353	signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	5516.82	5758.48	1.0438
2354	signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	5516.67	5758.22	1.04379
2355	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	5262.6	5492.58	1.0437
2356	signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	5515.12	5755.63	1.04361
2357	signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	5514.85	5755.17	1.04358
2358	signal transducer and activator of transcription 4. [swissprot;acc:q14765]	5514.83	5755.14
2359	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	5514.81	5755.1	1.04357
2360	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	3843.06	3682.72	1.04354
2361	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	4674.38	4877.31	1.04341
2362	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	4673.96	4876.71	1.04338

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.