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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2408 to 2457 of 3228 in total 
    Value Type	Measured
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
2408	serpin b11. [source:swissprot;acc:q96p15]	5078.5	5275.76	1.03884	
2409	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [source:swissprot;acc:p35237]	5078.5	5275.76	1.03884	
2410	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	5078.5	5275.76	1.03884	
2411	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [source:swissprot;acc:p30740]	5078.5	5275.76	1.03884	
2412	dynactin 4. [source:refseq;acc:nm_032486]	4644.04	4470.47	1.03883	
2413	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [source:refseq;acc:nm_004059]	6956.32	7223.14	1.03836	
2414	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [source:refseq;acc:nm_133443]	6956.32	7223.14	1.03836	
2415	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	6956.62	7223.09	1.0383	
2416	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [source:refseq;acc:nm_006442]	8048.38	7752.09	1.03822	
2417	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	3598.55	3467.65	1.03775	
2418	60s acidic ribosomal protein p1. [source:swissprot;acc:p05386]	4857.03	5039.78	1.03763	
2419	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [source:refseq;acc:nm_032243]	4857.03	5039.78	1.03763	
2420	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [source:swissprot;acc:p10599]	4857.03	5039.78	1.03763	
2421	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	7355.46	7088.93	1.0376	
2422	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	7355.46	7088.93	1.0376	
2423	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	7355.46	7088.93	1.0376	
2424	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	7355.46	7088.93	1.0376	
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	

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/