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911.
Curtis Huttenhower Avi I Flamholz Jessica N Landis Sauhard Sahi Chad L Myers Kellen L Olszewski Matthew A Hibbs Nathan O Siemers Olga G Troyanskaya Hilary A Coller 《BMC bioinformatics》2007,8(1):250
Background
The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrated workings of the cell. However, translating this amount of data into biological insight remains a daunting task. An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes). 相似文献912.
HSF2 binds to the Hsp90, Hsp27, and c-Fos promoters constitutively and modulates their expression 总被引:1,自引:0,他引:1 下载免费PDF全文
Although the vast majority of genomic DNA is tightly compacted during mitosis, the promoter regions of a number of genes remain in a less compacted state throughout this stage of the cell cycle. The decreased compaction of these promoter regions, which is referred to as gene bookmarking, is thought to be important for the ability of cells to express these genes during the following interphase. Previously, we reported a role for the DNA-binding protein heat shock factor (HSF2) in bookmarking the stress-inducible 70,000-Da heat shock protein (hsp70) gene. In this report, we have extended those studies and found that during mitosis, HSF2 is bound to the HSE promoter elements of other heat shock genes, including hsp90 and hsp27, as well as the proto-oncogene c-fos. The presence of HSF2 is important for expression of these genes because blocking HSF2 levels by RNA interference techniques leads to decreased levels of these proteins. These results suggest that HSF2 is important for constitutive as well as stress-inducible expression of HSE-containing genes. 相似文献
913.
For many patients, the traditional biomedical model that physicians have used to manage chronic prostatitis does not work. This article describes innovative treatment strategies for chronic prostatitis/chronic pelvic pain syndrome, with an emphasis on novel biomedical physical therapy and biopsychosocial approaches to the management of individualized patient symptoms. 相似文献
914.
Hart-Smith G Lovestead TM Davis TP Stenzel MH Barner-Kowollik C 《Biomacromolecules》2007,8(8):2404-2415
"Smart" polymers and polymer-protein conjugates find a vast array of biomedical applications. Ambient temperature reversible addition fragmentation chain transfer (RAFT) polymerizations conducted in an aqueous environment are a favorable method of choice for the synthesis of these materials; however, information regarding the initiation mechanisms behind these polymerizations-and thus the critical polymer end groups-is lacking. In the current study, high-resolution soft ionization mass spectrometry techniques were used to map the product species generated during ambient temperature gamma-radiation induced RAFT polymerizations of N-isopropylacrylamide (NIPAAm) and acrylic acid (AA) in aqueous media, allowing the generated end groups to be unambiguously established. It was found that trithiocarbonate and *R radicals produced from the radiolysis of the RAFT agent, *OH and *OOH radicals produced from the radiolysis of water, and *H radicals produced from the radiolysis of water, RAFT agent, or monomer were capable of initiating polymerizations and thus contribute toward the generated chain ends. Additionally, thiol terminated chains were formed via degradation of trithiocarbonate end groups. The current study is the first to provide comprehensive mapping of the formation pathways and end group patterns of stimuli-responsive polymers, thus allowing the design and implementation of these materials to proceed in a more tailored fashion. 相似文献
915.
OBO-Edit--an ontology editor for biologists 总被引:3,自引:0,他引:3
Day-Richter J Harris MA Haendel M;Gene Ontology OBO-Edit Working Group Lewis S 《Bioinformatics (Oxford, England)》2007,23(16):2198-2200
OBO-Edit is an open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses a graph-oriented approach to display and edit ontologies. OBO-Edit is particularly valuable for viewing and editing biomedical ontologies. Availability: https://sourceforge.net/project/showfiles.php?group_id=36855. 相似文献
916.
Soybean aphid resistance genes in the soybean cultivars Dowling and Jackson map to linkage group M 总被引:4,自引:0,他引:4
Yan Li Curtis B. Hill Shawn R. Carlson Brian W. Diers Glen L. Hartman 《Molecular breeding : new strategies in plant improvement》2007,19(1):25-34
The soybean aphid [Aphis glycines Matsumura] is an important pest of soybean [Glycine max (L.) Merr.] in North America. Single dominant genes in the cultivars ‘Dowling’ and ‘Jackson’ control resistance to the soybean
aphid. The gene in Dowling was named Rag1, and the genetic relationship between Rag1 and the gene in Jackson is not known. The objectives of this study were to map the locations of Rag1 and the Jackson gene onto the soybean genetic map. Segregation of aphid resistance and simple sequence repeat (SSR) markers
in F
2:3 populations developed from crosses between Dowling and the two susceptible soybean cultivars ‘Loda’ and ‘Williams 82’, and
between Jackson and Loda, were analyzed. Both Rag1 and the Jackson gene segregated 1:2:1 in the F
2:3 populations and mapped to soybean linkage group M between the markers Satt435 and Satt463. Rag1 mapped 4.2 cM from Satt435 and 7.9 cM from Satt463. The Jackson gene mapped 2.1 cM from Satt435 and 8.2 cM from Satt463.
Further tests to determine genetic allelism between Rag1 and the Jackson gene are in progress. The SSR markers flanking these resistance genes are being used in marker-assisted selection
for aphid resistance in soybean breeding programs.
Trade and manufacturers’ names are necessary to report factually on available data; however, the USDA neither guarantees nor
warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion
of others that may also be suitable. 相似文献
917.
Zachary D. Stephens Skylar Y. Lee Faraz Faghri Roy H. Campbell Chengxiang Zhai Miles J. Efron Ravishankar Iyer Michael C. Schatz Saurabh Sinha Gene E. Robinson 《PLoS biology》2015,13(7)
Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.We compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Astronomy has faced the challenges of Big Data for over 20 years and continues with ever-more ambitious studies of the universe. YouTube burst on the scene in 2005 and has sparked extraordinary worldwide interest in creating and sharing huge numbers of videos. Twitter, created in 2006, has become the poster child of the burgeoning movement in computational social science [6], with unprecedented opportunities for new insights by mining the enormous and ever-growing amount of textual data [7]. Particle physics also produces massive quantities of raw data, although the footprint is surprisingly limited since the vast majority of data are discarded soon after acquisition using the processing power that is coupled to the sensors [8]. Consequently, we do not include the domain in full detail here, although that model of rapid filtering and analysis will surely play an increasingly important role in genomics as the field matures.To compare these four disparate domains, we considered the four components that comprise the “life cycle” of a dataset: acquisition, storage, distribution, and analysis (
Data Phase
Astronomy
Twitter
YouTube
Genomics
Acquisition
25 zetta-bytes/year 0.5–15 billion tweets/year 500–900 million hours/year 1 zetta-bases/year
Storage
1 EB/year 1–17 PB/year 1–2 EB/year 2–40 EB/year
Analysis
In situ data reduction Topic and sentiment mining Limited requirements Heterogeneous data and analysis Real-time processing Metadata analysis Variant calling, ~2 trillion central processing unit (CPU) hours Massive volumes All-pairs genome alignments, ~10,000 trillion CPU hours
Distribution
Dedicated lines from antennae to server (600 TB/s) Small units of distribution Major component of modern user’s bandwidth (10 MB/s) Many small (10 MB/s) and fewer massive (10 TB/s) data movement