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 2330 to 2379 of 3228 in total

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

Rank	description	red	green	network_comparison
2330	cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837]	6773.67	7075.51	1.04456
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
2363	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]	6822.6	6539.8	1.04324
2364	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506]
2365	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	5254.55	5480.56	1.04301
2366	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609]	5265.95	5492.28	1.04298
2367	fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]
2368	mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]
2369	fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]
2370	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]
2371	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	4668.29	4868.52	1.04289
2372	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	3677.53	3526.65	1.04278
2373	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
2374	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	3669.57	3520.86	1.04224
2375	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	3650.02	3502.81	1.04203
2376	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	3976.48	3816.38	1.04195
2377	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	3977.7	3818.01	1.04183
2378	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	3977.76	3818.09	1.04182
2379	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	3979.06	3819.84	1.04168

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.