TY - JOUR
T1 - lncHUB2
T2 - aggregated and inferred knowledge about human and mouse lncRNAs
AU - Marino, Giacomo B.
AU - Wojciechowicz, Megan L.
AU - Clarke, Daniel J.B.
AU - Kuleshov, Maxim V.
AU - Xie, Zhuorui
AU - Jeon, Minji
AU - Lachmann, Alexander
AU - Ma'ayan, Avi
N1 - Funding Information:
National Institutes of Health (NIH) (U24-CA264250,RC2-DK131995, R01-DK131525, U24-CA224260, T32-GM062754, OT2-OD030160). Funding for open access charge: NIH (U24-CA264250)
Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press.
PY - 2023
Y1 - 2023
N2 - Long non-coding ribonucleic acids (lncRNAs) account for the largest group of non-coding RNAs. However, knowledge about their function and regulation is limited. lncHUB2 is a web server database that provides known and inferred knowledge about the function of 18 705 human and 11 274 mouse lncRNAs. lncHUB2 produces reports that contain the secondary structure fold of the lncRNA, related publications, the most correlated coding genes, the most correlated lncRNAs, a network that visualizes the most correlated genes, predicted mouse phenotypes, predicted membership in biological processes and pathways, predicted upstream transcription factor regulators, and predicted disease associations. In addition, the reports include subcellular localization information; expression across tissues, cell types, and cell lines, and predicted small molecules and CRISPR knockout (CRISPR-KO) genes prioritized based on their likelihood to up- or downregulate the expression of the lncRNA. Overall, lncHUB2 is a database with rich information about human and mouse lncRNAs and as such it can facilitate hypothesis generation for many future studies. The lncHUB2 database is available at https://maayanlab.cloud/lncHUB2. Database URL: https://maayanlab.cloud/lncHUB2
AB - Long non-coding ribonucleic acids (lncRNAs) account for the largest group of non-coding RNAs. However, knowledge about their function and regulation is limited. lncHUB2 is a web server database that provides known and inferred knowledge about the function of 18 705 human and 11 274 mouse lncRNAs. lncHUB2 produces reports that contain the secondary structure fold of the lncRNA, related publications, the most correlated coding genes, the most correlated lncRNAs, a network that visualizes the most correlated genes, predicted mouse phenotypes, predicted membership in biological processes and pathways, predicted upstream transcription factor regulators, and predicted disease associations. In addition, the reports include subcellular localization information; expression across tissues, cell types, and cell lines, and predicted small molecules and CRISPR knockout (CRISPR-KO) genes prioritized based on their likelihood to up- or downregulate the expression of the lncRNA. Overall, lncHUB2 is a database with rich information about human and mouse lncRNAs and as such it can facilitate hypothesis generation for many future studies. The lncHUB2 database is available at https://maayanlab.cloud/lncHUB2. Database URL: https://maayanlab.cloud/lncHUB2
UR - http://www.scopus.com/inward/record.url?scp=85149594602&partnerID=8YFLogxK
U2 - 10.1093/database/baad009
DO - 10.1093/database/baad009
M3 - Article
C2 - 36869839
AN - SCOPUS:85149594602
SN - 1758-0463
VL - 2023
JO - Database : the journal of biological databases and curation
JF - Database : the journal of biological databases and curation
M1 - baad009
ER -