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 2425 to 2474 of 3228 in total

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

Rank	description	red	green	network_comparison	
2425	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	7355.46	7088.93	1.0376	
2426	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	6123.47	6351.84	1.03729	
2427	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [source:swissprot;acc:q9y399]	5333.6	5531.41	1.03709	
2428	fragile x mental retardation syndrome related protein 2. [source:swissprot;acc:p51116]	7243.19	7509.81	1.03681	
2429	fragile x mental retardation syndrome related protein 1. [source:swissprot;acc:p51114]	7243.19	7509.81	1.03681	
2430	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	7243.07	7509.58	1.0368	
2431	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [source:swissprot;acc:q06787]	7242.75	7508.98	1.03676	
2432	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	8154.48	8453.84	1.03671	
2433	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	4585.86	4753.26	1.0365	
2434	wd repeat domain 26. [source:refseq;acc:nm_025160]	6423.46	6655.9	1.03619	
2435	activator of camp-responsive element modulator (crem) in testis; lim protein act. [source:refseq;acc:nm_020482]	3669.33	3797.78	1.03501	
2436	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	3708.67	3584.47	1.03465	
2437	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	3708.67	3584.47	1.03465	
2438	rna, u transporter 1; snurportin-1. [source:refseq;acc:nm_005701]	7139.06	7384.85	1.03443	
2439	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	3754.39	3629.51	1.03441	
2440	u3 snornp protein 4 homolog. [source:refseq;acc:nm_033416]	4730.66	4891.26	1.03395	
2441	adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [source:swissprot;acc:p53677]	6477.82	6695.58	1.03362	
2442	breast cancer type 1 susceptibility protein. [source:swissprot;acc:p38398]	5454.62	5637.88	1.0336	
2443	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	3634.59	3756.67	1.03359	
2444	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [source:swissprot;acc:q9y2t2]	6478.14	6695.67	1.03358	
2445	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [source:swissprot;acc:q14192]	3633.14	3754.96	1.03353	
2446	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	4031.94	4166.99	1.0335	
2447	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	3730.53	3611.05	1.03309	
2448	40s ribosomal protein s16. [source:swissprot;acc:p17008]	3730.53	3611.05	1.03309	
2449	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	3730.74	3611.45	1.03303	
2450	pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [source:swissprot;acc:p11177]	6737.15	6957.34	1.03268	
2451	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [source:swissprot;acc:p12694]	6737.15	6957.34	1.03268	
2452	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [source:swissprot;acc:p31040]	6042.36	6237.19	1.03224	
2453	conserved oligomeric golgi complex component 6. [source:swissprot;acc:q9y2v7]	6931.15	7152.73	1.03197	
2454	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [source:swissprot;acc:q03014]	8751.01	8480.03	1.03196	
2455	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [source:refseq;acc:nm_024831]	5978.83	6166.89	1.03145	
2456	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [source:refseq;acc:nm_020399]	5978.83	6166.89	1.03145	
2457	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [source:refseq;acc:nm_014263]	4998.72	5155.87	1.03144	
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	

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/