A census of human RNA-binding proteins.
TL;DR: This work presents a census of 1,542 manually curated RBPs that are analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression, a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
read more
Abstract: Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Functional characterization of splicing regulatory elements
TL;DR: In this paper, the authors utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins, and identify features which make splicing events more sensitive to depletion of RNA binding protein, as well as which RNA-binding proteins act as splicing regulators sensitive to protein depletion.
Proteomic profiles associated with postsurgical progression in non-functioning pituitary adenomas.
Tobias Hallén,Gudmundur Johannsson,Annika Thorsell,Daniel S Olsson,Charlotte Örndal,Angelica Engvall,Frida Jacobson,Anna Widgren,Jonas Bergquist,Thomas Skoglund +9 more
TL;DR: This first exploratory study analyzing proteomic profiles as markers of postoperative tumor progression in NFPA clearly showed different profiles between tumors with indolent postoperative behavior and those with postoperative tumor progression.
2
Construction of a redox-related gene signature for overall survival prediction and immune infiltration in non-small-cell lung cancer
TL;DR: A prognostic redox-related gene signature was successfully established in NSCLC, with potential applications in the clinical setting, and the high-risk group was significantly correlated with worse overall survival (OS).
2
ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning
Angel Ruiz-Reche,Akanksha Srivastava,Joel A. Indi,Joel A. Indi,Ivan de la Rubia,Eduardo Eyras +5 more
TL;DR: ReorientExpress uses deep-learning to correctly predict the orientation of the majority of reads, and in particular when trained on a closely related species or in combination with read clustering, which enables long-read transcriptomics in non-model organisms and samples without a genome reference and without using additional technologies.
Systematic Construction and Validation of an RNA-Binding Protein-Associated Prognostic Model for Acute Myeloid Leukemia.
TL;DR: In this paper, the role of RNA-binding proteins (RBPs) in acute myeloid leukemia (AML) is investigated by using univariate Cox regression analysis, least absolute shrinkage and selection operator (LASSO)-Cox regression analysis and multivariate Cox regressions.
References
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
98.8K
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
36K
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Related Papers (5)
Debashish Ray,Hilal Kazan,Kate B. Cook,Matthew T. Weirauch,Matthew T. Weirauch,Hamed S. Najafabadi,Xiao Li,Serge Gueroussov,Mihai Albu,Hong Zheng,Ally Yang,Hong Na,Manuel Irimia,Leah H. Matzat,Ryan K. Dale,Sarah A. Smith,Christopher A. Yarosh,Seth M. Kelly,Behnam Nabet,D. Mecenas,Weimin Li,Rakesh S. Laishram,Mei Qiao,Howard D. Lipshitz,Fabio Piano,Anita H. Corbett,Russ P. Carstens,Brendan J. Frey,Richard A. Anderson,Kristen W. Lynch,Luiz O. F. Penalva,Elissa P. Lei,Andrew G. Fraser,Benjamin J. Blencowe,Quaid Morris,Timothy P. Hughes +35 more
[...]