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Methods: ECgene: Genome-based EST clustering and gene modeling for alternative splicing
- Namshin Kim,
- Seokmin Shin,
- and Sanghyuk Lee
Genome Res. April 2005 15: 566-576; doi:10.1101/gr.3030405
...or quantitative patterns of gene expression can be inferred by inspecting the tissue origin of the cDNA libraries comprising an EST cluster, as for example seen in the BodyMap project ( Kawamoto et al. 2000 ). Several well known EST clustering algorithms exist, most of which depend on pairwise alignment of ESTs...
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METHODS: The Comparison of Gene Expression from Multiple cDNA Libraries
- Dov J Stekel,
- Yoav Git,
- and Francesco Falciani
Genome Res. December 1, 2000 10: 2055-2061; Published in Advance November 21, 2000, doi:10.1101/gr.132500
...and therefore can detect only expression of a predefined set of genes. There are a growing number of cDNA library databases available both commercially and in the public domain. These include the BodyMap project ( Okubo et al. 1992 ; http://www.imcb.osaka-u.ac.jp/bodymap/ ) and Incyte's LifeSeq database ( http...
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LETTER: Comparative Analysis of Gene Expression for Convergent Evolution of Camera Eye Between Octopus and Human
- Atsushi Ogura,
- Kazuho Ikeo,
- and Takashi Gojobori
Genome Res. August 2004 14: 1555-1561; doi:10.1101/gr.2268104
...the three databases of BodyMap, the Mammalian Gene Collection (MGC), and the National Eye Institute NEIBank. First, we created a single set of genes from the three distinct databases of gene expression for the human eye (see Methods section). Next, we obtained full-length gene sequences by comparing...
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Method: High-confidence coding and noncoding transcriptome maps
- Bo-Hyun You,
- Sang-Ho Yoon,
- and Jin-Wu Nam
Genome Res. June 2017 27: 1050-1062; Published in Advance April 10, 2017, doi:10.1101/gr.214288.116
...(Djebali et al. 2012; Harrow et al. 2012). Intriguingly, a significant portion of these extensive transcription signals, mostly from intergenic regions, turned out to be unannotated. To identify the unannotated transcriptome, gene annotation projects, such as GENCODE (Harrow et al. 2012), Human BodyMap 2...
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Research: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
- Milana Frenkel-Morgenstern,
- Vincent Lacroix,
- Iakes Ezkurdia,
- Yishai Levin,
- Alexandra Gabashvili,
- Jaime Prilusky,
- Angela del Pozo,
- Michael Tress,
- Rory Johnson,
- Roderic Guigo,
- and Alfonso Valencia
Genome Res. July 2012 22: 1231-1242; Published in Advance May 15, 2012, doi:10.1101/gr.130062.111
...), as the chimeric reads by definition do not map to any location in the or to the annotated transcriptome. Among the 7224 ESTs and mRNAs in ChimerDB (Kim et al. 2010), we found that 333 (4.5%) had at least two matching reads from the Human BodyMap data set, 212 (3%) had matching reads in two tissues, and 156 (2...
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Research: Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
- Michael R. Tallack,
- Graham W. Magor,
- Benjamin Dartigues,
- Lei Sun,
- Stephen Huang,
- Jessica M. Fittock,
- Sally V. Fry,
- Evgeny A. Glazov,
- Timothy L. Bailey,
- and Andrew C. Perkins
Genome Res. December 2012 22: 2385-2398; Published in Advance July 26, 2012, doi:10.1101/gr.135707.111
...the IlluminaGAII sequencing platform for three independent biological samples of Klf1+/+ and Klf1#2;/ fetal liver. We collected greater than 20 million sequence reads for each sample and mapped these to the mouse (mm9). To determine a highly sensitive set of KLF1-dependent genes, we performed a differential...
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LETTER: A Comprehensive, High-Resolution Genomic Transcript Map of Human Skeletal Muscle
- Stefania Bortoluzzi,
- Luca Rampoldi,
- Barbara Simionati,
- Rosanna Zimbello,
- Alessandro Barbon,
- Fabio d’Alessi,
- Natascia Tiso,
- Alberto Pallavicini,
- Stefano Toppo,
- Nicola Cannata,
- Giorgio Valle,
- Gerolamo Lanfranchi,
- and Gian Antonio Danieli
Genome Res. August 1, 1998 8: 817-825; doi:10.1101/gr.8.8.817
...://agave.humgen.upenn.edu/lens ), Human Gene Index at TIGR ( http://www.tigr.org/tdb/hgi/searching/hgi_xpress_search.html ), BodyMap ( http://www.imcb.osaka-u.ac.jp/bodymap/welcome.html ), and sporadic attempts to construct low-resolution genomic maps ( Polymeropoulos et al. 1993 ; Hwang et al. 1997 ) or transcript maps of individual...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...curated gene annotations that will inform infectious disease and transplantation research.Rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques are the most widely used nonhuman primate models for infectious disease and transplantation research (Anderson and Kirk 2013; Burwitz et al. 2017...
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Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
...genes was performed across Anopheline species, using OrthoDB (Kriventseva et al. 2015). The level of conservation was similar for both the known and novel protein coding regions of the (Supplemental Information Fig. B). Figure 3C shows identification of one such novel protein-coding gene, which showed...
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Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
- Tsung-Cheng Chang,
- Mihaela Pertea,
- Sungyul Lee,
- Steven L. Salzberg,
- and Joshua T. Mendell
Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
...to determine whether they could be used for this purpose. The Illumina BodyMap 2.0 represents a collection of RNA-seq data sets generated from 16 human tissues, each sequenced very deeply (∼80 million 50-bp pairedend reads per sample) (www.ebi.ac.uk/arrayexpress; ArrayExpress ID: E-MTAB-513). As described...

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