Distinguishing protein-coding and noncoding genes in the human genome

By Michele E. Clamp, B. Fry, Michael Kamal, Xiaohui S. Xie, James A. Cuff, Michael F. Lin, Manolis Kellis, Kerstin Lindblad-Toh, Eric S. Lander. Proceedings of the National Academy of Sciences of the United States of America, 2007

652 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/01ca0859d76b8a56e815d275022fc2ed2290943a

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Citations in the corpus

The GENCODE pseudogene resource (2012, background): “The number of genes annotated in the genome has steadily dropped with the improvement in annotation [39].”
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. (2009, methodology): “Previous work has shown that 98% of the well-studied human genes have RFC scores > 90 (Clamp et al. 2007).”
Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life (2012, background): “For example, the number of proteins encoded by the human genome is remarkably similar to the number of proteins in the proteome of the Caenorhabditis elegans nematode, 20,000 (Clamp et al., 2007), and this number is comparable to the proteome size of several other eukaryotes (Claverie, 2001).”
A high-resolution map of human evolutionary constraint using 29 mammals (2011, positive): “Despite intense efforts to annotate protein-coding genes over the past decade 20,22-24 , we detected 3,788 candidate new exons (a 2% increase) using evolutionary signatures characteristic of protein-coding exons 25 .”
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies* (2008, background): “Altogether 5067 genes have been analyzed, corresponding to 25% of all the predicted protein-coding genes of the human genome (1).”
Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications (2016, background): “RNA-seq and NGS has confirmed that 98% of the human genome is transcribed from noncoding genomic regions, that only about 2% of the human genome codes for peptides and proteins with about 20,000 distinct proteincoding genes, and that alternative splicing seems to occur for 90% of protein-coding gene”
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities (2008, neutral): “Given the problems of relying solely upon ORF size, an alternative approach to discriminating long ncRNAs from mRNAs is to assess putative ORFs for similarity to known proteins or protein domains, since such homology provides in”
Ensembl 2009 (2008, neutral): “One new computational approach, which is being built on within GENCODE, is to use alignments across the many mammalian genomes now available to evaluate the conservation of putative coding sequences (25).”
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions (2010, methodology): “In addition to classifying novel transcript models, such methods also have applications in evaluating and revising existing gene annotations [2, 3, 4, 5, 6], and as input features for de novo gene structure predictors [7, 8].”
The Human Protein Atlas—a tool for pathology (2008, background): “Sequencing of the human genome has revealed approximately 20 500 protein encoding genes [1] and, consequently, it is now possible to envision a gene-centric proteomics approach to mapping the proteomic landscape of the human body [2].”