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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Gene	Value Type	Network Comparison Type	Rank	network_comparison	Interaction Map	red	description	green	Filtered

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Showing element 2318 to 2367 of 3228 in total

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

Rank	network_comparison	red	description	green
2318	1.04491	7484.98	ubiquitin. [swissprot;acc:p02248]	7821.11
2319	1.04478	6362.48	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	6647.42
2320			t54 protein. [swissprot;acc:q92917]
2321	1.04464	3496.21	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9]	3652.28
2322	1.04456	6773.67	mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796]	7075.51
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	1.04428	5123.89	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	5350.78
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	1.04421	5607.81	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1]	5855.72
2341	1.0442	5606.66	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]	5854.45
2342	1.04416	7007.72	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	7317.15
2343	1.04413	3672.17	40s ribosomal protein s5. [swissprot;acc:p46782]	3516.98
2344	1.04406	8353.97	carboxypeptidase a5. [refseq;acc:nm_080385]	8001.45
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		6480.27	ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	6765.81
2348			ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
2349		8353.97	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	8001.45
2350		6480.27	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]	6765.81
2351		8353.97	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	8001.45
2352	1.04402	8493.7	coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579]	8135.59
2353	1.0438	5516.82	signal transducer and activator of transcription 5b. [swissprot;acc:p51692]	5758.48
2354	1.04379	5516.67	signal transducer and activator of transcription 5a. [swissprot;acc:p42229]	5758.22
2355	1.0437	5262.6	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]	5492.58
2356	1.04361	5515.12	signal transducer and activator of transcription 6 (il-4 stat). [swissprot;acc:p42226]	5755.63
2357	1.04358	5514.85	signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	5755.17
2358		5514.83	signal transducer and activator of transcription 4. [swissprot;acc:q14765]	5755.14
2359	1.04357	5514.81	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [swissprot;acc:p42224]	5755.1
2360	1.04354	3843.06	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	3682.72
2361	1.04341	4674.38	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]	4877.31
2362	1.04338	4673.96	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]	4876.71
2363	1.04324	6822.6	glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507]	6539.8
2364			glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506]
2365	1.04301	5254.55	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	5480.56
2366	1.04298	5265.95	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609]	5492.28
2367			fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]

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.