Cargando…

Pharos 2023: an integrated resource for the understudied human proteome

The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort ar...

Descripción completa

Detalles Bibliográficos
Autores principales: Kelleher, Keith J, Sheils, Timothy K, Mathias, Stephen L, Yang, Jeremy J, Metzger, Vincent T, Siramshetty, Vishal B, Nguyen, Dac-Trung, Jensen, Lars Juhl, Vidović, Dušica, Schürer, Stephan C, Holmes, Jayme, Sharma, Karlie R, Pillai, Ajay, Bologa, Cristian G, Edwards, Jeremy S, Mathé, Ewy A, Oprea, Tudor I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825581/
https://www.ncbi.nlm.nih.gov/pubmed/36624666
http://dx.doi.org/10.1093/nar/gkac1033
_version_ 1784866664542633984
author Kelleher, Keith J
Sheils, Timothy K
Mathias, Stephen L
Yang, Jeremy J
Metzger, Vincent T
Siramshetty, Vishal B
Nguyen, Dac-Trung
Jensen, Lars Juhl
Vidović, Dušica
Schürer, Stephan C
Holmes, Jayme
Sharma, Karlie R
Pillai, Ajay
Bologa, Cristian G
Edwards, Jeremy S
Mathé, Ewy A
Oprea, Tudor I
author_facet Kelleher, Keith J
Sheils, Timothy K
Mathias, Stephen L
Yang, Jeremy J
Metzger, Vincent T
Siramshetty, Vishal B
Nguyen, Dac-Trung
Jensen, Lars Juhl
Vidović, Dušica
Schürer, Stephan C
Holmes, Jayme
Sharma, Karlie R
Pillai, Ajay
Bologa, Cristian G
Edwards, Jeremy S
Mathé, Ewy A
Oprea, Tudor I
author_sort Kelleher, Keith J
collection PubMed
description The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for users to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.
format Online
Article
Text
id pubmed-9825581
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-98255812023-01-10 Pharos 2023: an integrated resource for the understudied human proteome Kelleher, Keith J Sheils, Timothy K Mathias, Stephen L Yang, Jeremy J Metzger, Vincent T Siramshetty, Vishal B Nguyen, Dac-Trung Jensen, Lars Juhl Vidović, Dušica Schürer, Stephan C Holmes, Jayme Sharma, Karlie R Pillai, Ajay Bologa, Cristian G Edwards, Jeremy S Mathé, Ewy A Oprea, Tudor I Nucleic Acids Res Database Issue The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for users to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts. Oxford University Press 2022-11-29 /pmc/articles/PMC9825581/ /pubmed/36624666 http://dx.doi.org/10.1093/nar/gkac1033 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Kelleher, Keith J
Sheils, Timothy K
Mathias, Stephen L
Yang, Jeremy J
Metzger, Vincent T
Siramshetty, Vishal B
Nguyen, Dac-Trung
Jensen, Lars Juhl
Vidović, Dušica
Schürer, Stephan C
Holmes, Jayme
Sharma, Karlie R
Pillai, Ajay
Bologa, Cristian G
Edwards, Jeremy S
Mathé, Ewy A
Oprea, Tudor I
Pharos 2023: an integrated resource for the understudied human proteome
title Pharos 2023: an integrated resource for the understudied human proteome
title_full Pharos 2023: an integrated resource for the understudied human proteome
title_fullStr Pharos 2023: an integrated resource for the understudied human proteome
title_full_unstemmed Pharos 2023: an integrated resource for the understudied human proteome
title_short Pharos 2023: an integrated resource for the understudied human proteome
title_sort pharos 2023: an integrated resource for the understudied human proteome
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825581/
https://www.ncbi.nlm.nih.gov/pubmed/36624666
http://dx.doi.org/10.1093/nar/gkac1033
work_keys_str_mv AT kelleherkeithj pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT sheilstimothyk pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT mathiasstephenl pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT yangjeremyj pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT metzgervincentt pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT siramshettyvishalb pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT nguyendactrung pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT jensenlarsjuhl pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT vidovicdusica pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT schurerstephanc pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT holmesjayme pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT sharmakarlier pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT pillaiajay pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT bologacristiang pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT edwardsjeremys pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT matheewya pharos2023anintegratedresourcefortheunderstudiedhumanproteome
AT opreatudori pharos2023anintegratedresourcefortheunderstudiedhumanproteome