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 2458 to 2507 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2458	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	4751.74	4900.37	1.03128	
2459	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	4751.74	4900.37	1.03128	
2460	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	4751.74	4900.37	1.03128	
2461	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	5114.15	5272.92	1.03105	
2462	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	5114.15	5272.92	1.03105	
2463	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	5114.15	5272.92	1.03105	
2464	dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.12) (e2) (pdc-e2) (70 kda mitochondrial autoantigen of primary biliary cirrhosis) (pbc) (m2 antigen complex 70 kda subunit). [source:swissprot;acc:p10515]	6291.2	6486.07	1.03098	
2465	germ cell-less. [source:refseq;acc:nm_022471]	7764.92	8003.67	1.03075	
2466	pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [source:swissprot;acc:p40424]	7765.3	8004	1.03074	
2467	pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [source:swissprot;acc:p40426]	7765.3	8004	1.03074	
2468	hyporthetical protein mgc27169. [source:refseq;acc:nm_176782]	7765.3	8004	1.03074	
2469	homeobox protein meis1. [source:swissprot;acc:o00470]	7765.3	8004	1.03074	
2470	homeobox protein meis2 (meis1-related protein 1). [source:swissprot;acc:o14770]	7765.3	8004	1.03074	
2471	bag-family molecular chaperone regulator-2. [source:swissprot;acc:o95816]	7765.3	8004	1.03074	
2472	pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [source:swissprot;acc:p40425]	7765.3	8004	1.03074	
2473	pre-b-cell leukemia transcription factor 4. [source:refseq;acc:nm_025245]	7765.3	8004	1.03074	
2474	homeobox protein meis3 (meis1-related protein 2) (fragment). [source:swissprot;acc:q99687]	7765.3	8004	1.03074	
2475	zinc finger protein 444; endothelial zinc finger protein 2. [source:refseq;acc:nm_018337]	3573.66	3682.14	1.03036	
2476	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [source:swissprot;acc:q96gc6]	3569.07	3676.7	1.03016	
2477	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	3568.84	3676.43	1.03015	
2478	zinc finger protein 232. [source:swissprot;acc:q9uny5]	3568.96	3676.57	1.03015	
2479	zinc finger protein 99. [source:refseq;acc:nm_032164]	3568.99	3676.6	1.03015	
2480	zinc finger protein 305. [source:swissprot;acc:o43309]	3568.95	3676.56	1.03015	
2481	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	3568.8	3676.39	1.03015	
2482	zinc finger protein 213 (putative transcription factor cr53). [source:swissprot;acc:o14771]	3568.99	3676.61	1.03015	
2483	zinc finger protein 18 (zinc finger protein kox11) (fragment). [source:swissprot;acc:p17022]	3568.8	3676.38	1.03014	
2484	zinc finger imprinted 2. [source:swissprot;acc:q9nzv7]	3568.45	3675.97	1.03013	
2485	zinc finger protein 174 (aw-1). [source:swissprot;acc:q15697]	3568.18	3675.65	1.03012	
2486	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [source:swissprot;acc:o43708]	3626.38	3734.8	1.0299	
2487	tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [source:swissprot;acc:p18074]	6963.12	7170.02	1.02971	
2488	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [source:swissprot;acc:q07244]	5637.59	5804.47	1.0296	
2489	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [source:swissprot;acc:o43172]	5637.59	5804.47	1.0296	
2490	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	6294.37	6472.9	1.02836	
2491	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	3436.65	3531.96	1.02773	
2492	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	3436.65	3531.96	1.02773	
2493	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	3436.65	3531.96	1.02773	
2494	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	3436.65	3531.96	1.02773	
2495	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	3436.65	3531.96	1.02773	
2496	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	5534.46	5684.97	1.0272	
2497	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	7002.3	7192.25	1.02713	
2498	helicase (fragment). [source:sptrembl;acc:q92771]	7002.03	7191.88	1.02711	
2499	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	8186.02	7971.27	1.02694	
2500	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	3804.53	3705.05	1.02685	
2501	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p49448]	6562.71	6738.23	1.02675	
2502	glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [source:swissprot;acc:p00367]	6562.71	6738.23	1.02675	
2503	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [source:swissprot;acc:p53597]	5996.06	6155.81	1.02664	
2504	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [source:swissprot;acc:q9p2r7]	5996.06	6155.81	1.02664	
2505	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	6237.83	6400.74	1.02612	
2506	2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [source:swissprot;acc:q02218]	6200.39	6362.25	1.0261	
2507	mevalonate kinase (ec 2.7.1.36) (mk). [source:swissprot;acc:q03426]	4243.44	4352.56	1.02571	

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/