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

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 2358 to 2407 of 3228 in total

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

Rank	description	red	green	network_comparison	
2358	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	5514.83	5755.14	1.04358	
2359	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	5514.81	5755.1	1.04357	
2360	60s ribosomal protein l4 (l1). [source: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. [source: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. [source: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). [source: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). [source:swissprot;acc:p48506]	6822.6	6539.8	1.04324	
2365	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source: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). [source: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. [source:refseq;acc:nm_021727]	5265.95	5492.28	1.04298	
2368	mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [source:swissprot;acc:q13485]	5265.95	5492.28	1.04298	
2369	fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [source:refseq;acc:nm_004265]	5265.95	5492.28	1.04298	
2370	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	5265.95	5492.28	1.04298	
2371	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [source:swissprot;acc:p52435]	4668.29	4868.52	1.04289	
2372	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	3677.53	3526.65	1.04278	
2373	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	3677.53	3526.65	1.04278	
2374	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source: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). [source:swissprot;acc:q9y606]	3650.02	3502.81	1.04203	
2376	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	3976.48	3816.38	1.04195	
2377	likely ortholog of mouse shc sh2-domain binding protein 1. [source: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). [source:swissprot;acc:q16527]	3977.76	3818.09	1.04182	
2379	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	3979.06	3819.84	1.04168	
2380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source: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). [source: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). [source: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). [source: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). [source:swissprot;acc:p07384]	4164.96	4336.92	1.04129	
2385	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	3716.43	3569.68	1.04111	
2386	60s ribosomal protein l30. [source:swissprot;acc:p04645]	3674.02	3529.35	1.04099	
2387	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	8265.85	7940.87	1.04092	
2388	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [source:swissprot;acc:p53602]	4418.21	4594.87	1.03998	
2389	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [source:swissprot;acc:q9y234]	6327.14	6579.38	1.03987	
2390	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [source:swissprot;acc:p23258]	6327.14	6579.38	1.03987	
2391	defender against cell death 1 (dad-1). [source:swissprot;acc:p46966]	6327.14	6579.38	1.03987	
2392	t-complex 11. [source:refseq;acc:nm_018679]	6327.14	6579.38	1.03987	
2393	tubulin gamma-2 chain (gamma-2 tubulin). [source:swissprot;acc:q9nrh3]	6327.14	6579.38	1.03987	
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)]. [source:swissprot;acc:p22102]	5502.5	5721.43	1.03979	
2395	homeobox protein otx2. [source: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. [source:refseq;acc:nm_022572]	6711.27	6974.49	1.03922	
2397	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	6707.29	6970.07	1.03918	
2398	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	6707.29	6970.07	1.03918	
2399	homeobox protein otx1. [source:swissprot;acc:p32242]	5691.1	5913.92	1.03915	
2400	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	4368.44	4539.34	1.03912	
2401	cone-rod homeobox protein. [source:swissprot;acc:o43186]	5694.04	5916.78	1.03912	
2402	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [source:swissprot;acc:p08865]	5078.5	5275.76	1.03884	
2403	40s ribosomal protein s21. [source:swissprot;acc:p35265]	5078.5	5275.76	1.03884	
2404	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [source:swissprot;acc:p50453]	5078.5	5275.76	1.03884	
2405	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	5078.5	5275.76	1.03884	
2406	bomapin (protease inhibitor 10) (serpin b10). [source:swissprot;acc:p48595]	5078.5	5275.76	1.03884	
2407	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [source:swissprot;acc:p05120]	5078.5	5275.76	1.03884	

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/