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APPRIS 2017: principal isoforms for multiple gene sets

Jose Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L Tress
2017 Nucleic Acids Research  
APPRIS selects a single protein isoform, the 'principal' isoform, as the reference for each gene based on these annotations.  ...  A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms.  ...  The merged Intersection gene set allows us to identify principal isoforms missing in the individual gene sets.  ... 
doi:10.1093/nar/gkx997 pmid:29069475 pmcid:PMC5753224 fatcat:dmhn5ropvnbtzoftrf4aoovvoe

Alternative Splicing May Not Be the Key to Proteome Complexity

Michael L. Tress, Federico Abascal, Alfonso Valencia
2017 TIBS -Trends in Biochemical Sciences. Regular ed  
Many estimates for the number of transcripts expressed in human cells are even higher; a recent large-scale RNA-seq analysis [3] found multiple splice variants for 72% of annotated human genes, while another  ...  The clearest finding from proteomics experiments is that most human genes have a single main protein isoform, while those alternative isoforms that are identified tend to be the most biologically plausible  ...  Acknowledgments The authors would like to thank Iakes Ezkurdia for his input on the paper. This work was supported by the National Institutes of Health (NIH, Grant No. U41 HG007234).  ... 
doi:10.1016/j.tibs.2016.08.008 pmid:27712956 fatcat:andwmtj3rfclpowwqbjhu4ik2u

Transcript Isoform Differences Across Human Tissues Are Predominantly Driven By Alternative Start And Termination Sites Of Transcription [article]

Alejandro Reyes, Wolfgang Huber
2017 bioRxiv   pre-print
Most human genes have multiple transcription start and polyadenylation sites, as well as alternatively spliced exons.  ...  Our analysis identifies transcription start and termination sites as the principal drivers of isoform diversity across tissues.  ...  Acknowledgements We would like to thank Alvis Brazma and Vicent Pelechano for critical reading of this manuscript. We thank the GTEx and FANTOM consortiums for providing access to their data.  ... 
doi:10.1101/127894 fatcat:ims47h2q55gktapqou3ar6yi24

Network-based method for drug target discovery at the isoform level

Jun Ma, Jenny Wang, Laleh Soltan Ghoraie, Xin Men, Linna Liu, Penggao Dai
2019 Scientific Reports  
We further analyzed the properties of target major isoforms for each multi-isoform gene using pharmacogenomic datasets, proteomic data and the principal isoforms defined by the APPRIS and STRING datasets  ...  Interestingly, these isoforms are not annotated as principal isoforms in APPRIS. Lastly, we tested the affinity of the target major isoform of MGEA5 for streptozocin through in silico docking.  ...  Acknowledgements The author thanks Petr Smirov, Zhaleh Safikhani and Seyed Ali Madani Tonekaboni for helpful advice and discussion about building co-expression network at isoform level, drug sensitivity  ... 
doi:10.1038/s41598-019-50224-x pmid:31554914 pmcid:PMC6761107 fatcat:n22wlxq5ybf67gh6bp3eft4iai

The distribution pattern of genetic variation in the transcript isoforms of the alternatively spliced protein-coding genes in the human genome

Ting Liu, Kui Lin
2015 Molecular Biosystems  
Acknowledgements We thank the two anonymous reviewers for their valuable suggestions and comments.  ...  We are grateful to Zhen Li, Erli Pang, Tao Zhu, Jia Song and Professor Deng-Ke Niu for their helpful discussions and suggestions. We could not have finished this study without your help.  ...  The principal isoforms were assigned in accordance with APPRIS annotations. For those genes without a clear principal isoform prediction, we used their longest candidates according to APPRIS.  ... 
doi:10.1039/c5mb00132c pmid:25820936 fatcat:w2g3fi25sfe5vjhqqfowolzq3y

Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

Jae Yong Ryu, Hyun Uk Kim, Sang Yup Lee
2017 Proceedings of the National Academy of Sciences of the United States of America  
The framework in this study generated 11,415 GeTPRA corresponding to 1,106 metabolic genes for both principal and nonprincipal transcripts (PTs and NPTs) of metabolic genes.  ...  Alternative splicing plays important roles in generating different transcripts from one gene, and consequently various protein isoforms.  ...  This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557) from the Ministry  ... 
doi:10.1073/pnas.1713050114 pmid:29078384 pmcid:PMC5692585 fatcat:cvy7juv4mjh77iv7mf57oqi6la

Clinical Annotation Reference Templates: a resource for consistent variant annotation

Shawn Yost, Márton Münz, Shazia Mahamdallie, Anthony Renwick, Elise Ruark, Nazneen Rahman
2018 Wellcome Open Research  
Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38.  ...  Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available.  ...  Acknowledgements We are very grateful to the many different people we had helpful discussions with over the last three years as we were developing the CARTs, in particular within the TGMI, EBI, APPRIS,  ... 
doi:10.12688/wellcomeopenres.14924.1 fatcat:g4khooyiqfbynguuwwp4hvw4jq

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

Javier Tapial, Kevin C.H. Ha, Timothy Sterne-Weiler, André Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang (+6 others)
2017 Genome Research  
Isoforms encoded by the latter set of genes are generally coexpressed in the same cells and are often engaged by translating ribosomes.  ...  Contrary to recent reports concluding that nearly all human genes express a single major isoform, VastDB provides evidence that at least 48% of multiexonic protein-coding genes express multiple splice  ...  model validation, Lawrence Kelley and Michael Sternberg for privileged access to the Phyre2 server, and the Donnelly Sequencing Centre for generating RNA-seq data for this study.  ... 
doi:10.1101/gr.220962.117 pmid:28855263 pmcid:PMC5630039 fatcat:z3jemnx4jrgjvn4nglafwm3vuy

SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification [article]

Manuel Tardaguila, Lorena de la Fuente, Cristina Marti, Cecile Pereira, Francisco Jose Pardo-Palacios, Hector del Risco, Marc Ferrell, Maravillas Mellado, Marissa Macchietto, Kenneth Verheggen, Mariola Edelmann, Iakes Ezkurdia (+7 others)
2017 biorxiv/medrxiv   pre-print
isoform of their genes.  ...  Nonetheless, there is a need for studies and tools that characterize these novel isoforms.  ...  Acknowledgments We thank Eric Triplett (University of Florida) for support in sequencing experiments and Elizabeth Tseng (PacBio) for helping in running the ToFU pipeline and critically reading this manuscript  ... 
doi:10.1101/118083 fatcat:f5uehdqxjjgclbk4j3dlbtiszi

GENCODE reference annotation for the human and mouse genomes

Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong, If Barnes, Andrew Berry (+43 others)
2018 Nucleic Acids Research  
The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics  ...  Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines.  ...  ACKNOWLEDGEMENTS We thank Tim Hubbard and Jennifer Harrow for their leadership in the GENCODE project from 2003-2016 as well as all groups and group members involved in the GENCODE project since its inception  ... 
doi:10.1093/nar/gky955 pmid:30357393 pmcid:PMC6323946 fatcat:vg5kuecy5rc7xewce5u3xczdba

Transcripts evolutionary conservation and structural dynamics give insights into the role of alternative splicing for the JNK family [article]

Adel Ait-hamlat, Lelia Polit, Hugues Richard, Elodie Laine
2017 bioRxiv   pre-print
Alternative splicing (AS), by producing several transcript isoforms from the same gene, has the potential to greatly expand the proteome in eukaryotes.  ...  Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool that infers plausible evolutionary scenarios explaining a set of transcripts  ...  A forest structure S is fixed by 552 setting n b , n l and n r the respective numbers of binary, left and right subnodes for every internal 553 node of the gene tree.  ... 
doi:10.1101/119891 fatcat:cnyk3rk53ve6jggdzwoqh745pq

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes, Daniel Gautheret
2017 Genome Biology  
Acknowledgments We thank Damien Drubay for useful statistical discussions, William Ritchie and Lucile Broseus for running IRFinder, Haoliang Xue and Thibault Dayris for setting up the 1-transcript/gene  ...  reference transcriptome, and Jean-Marc Holder for English proofreading.  ...  Principal transcripts for protein-coding genes are extracted from the APPRIS database [43] . When several isoforms have the same principal level, the longest one is selected.  ... 
doi:10.1186/s13059-017-1372-2 pmid:29284518 pmcid:PMC5747171 fatcat:3mhh4ekdhvdbbdtc2q66uennum

Isoform-level gene expression patterns in single-cell RNA-sequencing data

Trung Nghia Vu, Quin F Wills, Krishna R Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan, Mattias Rantalainen, Janet Kelso
2018 Bioinformatics  
Results: We define six principal patterns of isoform expression relationships and describe a method for differential-pattern analysis.  ...  We assigned the pattern types to each of 16 562 isoform-pairs from 4929 genes.  ...  Acknowledgement We acknowledge Dr Aaron Diaz, the UCSF Principal Investigator for access permission to the brain tumor dataset deposited at the European Genomephenome Archive under accession number EGAS00001001900  ... 
doi:10.1093/bioinformatics/bty100 pmid:29490015 pmcid:PMC6041805 fatcat:67pqyb35cbbnnjl3hhg6xjyx4u

An analysis of tissue-specific alternative splicing at the protein level

Jose Manuel Rodriguez, Fernando Pozo, Tomas di Domenico, Jesus Vazquez, Michael L. Tress, Christine A. Orengo
2020 PLoS Computational Biology  
Here we investigated the evidence for tissue-specific splicing among splice isoforms detected in a large-scale proteomics analysis.  ...  By way of contrast, three in four alternative exons in the human gene set arose in the primate lineage, so our results cannot be extrapolated to the whole genome.  ...  Acknowledgments The authors would like to thank Federico Abascal for his invaluable input on this paper. Author Contributions Conceptualization: Michael L. Tress.  ... 
doi:10.1371/journal.pcbi.1008287 pmid:33017396 pmcid:PMC7561204 fatcat:5azcpwtg7bacnpiwbfqytxdr3e

Perturbation robustness analyses reveal important parameters in variant interpretation pipelines [article]

Yaqiong Wang, Aashish N Adhikari, Uma Sunderam, Mark N Kvale, Robert J Currier, Renata C Gallagher, Pui-Yan Kwok, Jennifer M Puck, Rajgopal Srinivasan, Steven E Brenner
2020 bioRxiv   pre-print
For this application, we perturbed commonly used parameters in variant interpretation pipelines, including choices of genes, variant callers, transcript models, databases of allele frequencies, databases  ...  A systematic approach for exploring parameter choices and selection plays an important role in designing robust pipelines for specific clinical applications.  ...  Acknowledgements We thank John-Marc Chandonia, Jingqi Chen, Zhiqiang Hu and Andrew Sharo for insightful discussions about this research.  ... 
doi:10.1101/2020.06.29.173815 fatcat:gzmob5mj75cmnayp3pwsvzgjj4
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