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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
...HGR as a powerful computational instrument for efficient and accurate cell annotation. Moreover, we illustrate the versatility of scHGR in supporting downstream analyses, such as differential gene expression (DEG) analysis, subtype revealing, Gene Ontology (GO) enrichment, and cell communication inference...
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METHODS: Predicting Gene Function From Patterns of Annotation
- Oliver D. King,
- Rebecca E. Foulger,
- Selina S. Dwight,
- James V. White,
- and Frederick P. Roth
Genome Res. May 1, 2003 13: 896-904; Published in Advance April 14, 2003, doi:10.1101/gr.440803
...) Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 12 : 203 – 214 . ↵ Schug J. , Diskin S. , Mazzarelli J. , Brunk B.P. , Stoeckert C.J. , Jr. ( 2002 ) Predicting gene ontology functions from ProDom and CDD protein domains. Genome Res. 12 : 648...
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METHODS: Using Text Analysis to Identify Functionally Coherent Gene Groups
- Soumya Raychaudhuri,
- Hinrich Schütze,
- and Russ B. Altman
Genome Res. October 1, 2002 12: 1582-1590; doi:10.1101/gr.116402
.... , Chang J.T. , Sutphin P.D. , Altman R.B. ( 2002 ) Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 12 : 203 – 214 . ↵ Roberts R.J. , Varmus H.E. , Ashburner M. , Brown P.O. , Eisen M.B. , Khosla C. , Kirschner M. , Nusse R. , Scott M...
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Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
...matching that of the literature. The reason it did not reach 1.00 can be attributed to four misannotated mRNAs in the set of zygotic transcripts. The red dot represents the eluate/flowthrough threshold of 0.5, which was used to identify zygotic transcripts in subsequent analyses.As more genes became...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...to expectations based on a trinucleotide model of mutation rate (Samocha et al. 2014) across different sets of genes (DD-associated with dominant or recessive mechanisms, and non-DD–associated; see Methods). Across recessive DD and non-DD–associated genes, no enrichment of DNMs beyond the expectation...
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Methods: Ab initio identification of functionally interacting pairs of cis-regulatory elements
- Brad A. Friedman,
- Michael B. Stadler,
- Noam Shomron,
- Ye Ding,
- and Christopher B. Burge
Genome Res. October 2008 18: 1643-1651; Published in Advance September 17, 2008, doi:10.1101/gr.080085.108
.... Expression of most human genes requires extensive splicing of primary RNA transcripts to produce mature protein-coding mRNAs. At the core of pre-mRNA splicing are tandem chemical reactions in which pairs of sequence elements—first the branch point and 5′ splice site (5′ss), then the 5′ss and 3′ splice site...
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RESOURCE: Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
- Takeshi Nagashima,
- Diego G. Silva,
- Nikolai Petrovsky,
- Luis A. Socha,
- Harukazu Suzuki,
- Rintaro Saito,
- Takeya Kasukawa,
- Igor V. Kurochkin,
- Akihiko Konagaya,
- and Christian Schönbach
Genome Res. June 2003 13: 1520-1533; doi:10.1101/gr.1019903
...) that are not linked with a gene. In contrast, G2D ( Perez-Iratxeta et al. 2002 ) extracts disease and substance Medical Subject Heading (MeSH) from MEDLINE articles associated with a mapped human gene and computationally infers gene ontology (GO) terms ( Ashburner et al. 2000 ) based on substance MeSH. The combined...
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Resource: The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program
- Olivier Tassy,
- Delphine Dauga,
- Fabrice Daian,
- Daniel Sobral,
- François Robin,
- Pierre Khoueiry,
- David Salgado,
- Vanessa Fox,
- Danièle Caillol,
- Renaud Schiappa,
- Baptiste Laporte,
- Anne Rios,
- Guillaume Luxardi,
- Takehiro Kusakabe,
- Jean-Stéphane Joly,
- Sébastien Darras,
- Lionel Christiaen,
- Magali Contensin,
- Hélène Auger,
- Clément Lamy,
- Clare Hudson,
- Ute Rothbächer,
- Michael J. Gilchrist,
- Kazuhiro W. Makabe,
- Kohji Hotta,
- Shigeki Fujiwara,
- Nori Satoh,
- Yutaka Satou,
- and Patrick Lemaire
Genome Res. October 2010 20: 1459-1468; Published in Advance July 20, 2010, doi:10.1101/gr.108175.110
...queries identified genes coding for secreted proteins (Gene Ontology query) and expressed during the cleavage stages (Digital Differential Display query). The set of anatomical queries identified the ancestor of the a6.5 cell pair, and then the vegetal neighbors of these animal cells. Integration...
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