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

Rank	description	red	green	network_comparison
2351	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	8353.97	8001.45	1.04406
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
2380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	3690.79	3543.33	1.04162
2381	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	3667.94	3521.41	1.04161
2382	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]	4457.6	4642.72	1.04153
2383	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	4164.76	4337.01	1.04136
2384	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	4164.96	4336.92	1.04129
2385	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	3716.43	3569.68	1.04111
2386	60s ribosomal protein l30. [swissprot;acc:p04645]	3674.02	3529.35	1.04099
2387	cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	8265.85	7940.87	1.04092
2388	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	4418.21	4594.87	1.03998
2389	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	6327.14	6579.38	1.03987
2390	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]
2391	defender against cell death 1 (dad-1). [swissprot;acc:p46966]
2392	t-complex 11. [refseq;acc:nm_018679]
2393	tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]
2394	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	5502.5	5721.43	1.03979
2395	homeobox protein otx2. [swissprot;acc:p32243]	5682	5905.08	1.03926
2396	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	6711.27	6974.49	1.03922
2397	yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	6707.29	6970.07	1.03918
2398	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
2399	homeobox protein otx1. [swissprot;acc:p32242]	5691.1	5913.92	1.03915
2400	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	4368.44	4539.34	1.03912

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.