TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool
The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, and its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to...
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| Veröffentlicht in: | PloS one 2022-09, Vol.17 (9), p.e0272302 |
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| creator | Christensen, Erik Naidas, Alaine Chen, David Husic, Mia Shooshtari, Parisa |
| description | The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, and its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to collect and present related TME data in an easily accessible format.
We therefore built a TME scRNA-seq database, and created the R package TMExplorer to facilitate investigation of the TME. TMExplorer provides an interface to easily access all available datasets and their metadata. The users can search for datasets using a thorough range of characteristics. The TMExplorer allows for examination of the TME using scRNA-seq in a way that is streamlined and allows for easy integration into already existing scRNA-seq analysis pipelines. |
| doi_str_mv | 10.1371/journal.pone.0272302 |
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We therefore built a TME scRNA-seq database, and created the R package TMExplorer to facilitate investigation of the TME. TMExplorer provides an interface to easily access all available datasets and their metadata. The users can search for datasets using a thorough range of characteristics. The TMExplorer allows for examination of the TME using scRNA-seq in a way that is streamlined and allows for easy integration into already existing scRNA-seq analysis pipelines.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0272302</identifier><identifier>PMID: 36084081</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Breast cancer ; Cancer ; Colorectal cancer ; Data collection ; Datasets ; Diagnosis ; Digital archives ; Fibroblasts ; Gastric cancer ; Gene expression ; Gene Expression Profiling ; Gene sequencing ; Genetic aspects ; Head & neck cancer ; Medical research ; Medicine and Health Sciences ; Metadata ; Microenvironments ; Online data bases ; Prostate cancer ; RNA ; Sequence Analysis, RNA ; Single-Cell Analysis ; Software ; Throat cancer ; Tumor microenvironment ; Tumor Microenvironment - genetics ; Tumors</subject><ispartof>PloS one, 2022-09, Vol.17 (9), p.e0272302</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Christensen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Christensen et al 2022 Christensen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c622t-ebb4215b65a78955efffdfe0a3c6366271172be129781ca2758e692849c110c73</citedby><cites>FETCH-LOGICAL-c622t-ebb4215b65a78955efffdfe0a3c6366271172be129781ca2758e692849c110c73</cites><orcidid>0000-0003-2273-1034</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462821/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462821/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36084081$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Deb, Sumitra</contributor><creatorcontrib>Christensen, Erik</creatorcontrib><creatorcontrib>Naidas, Alaine</creatorcontrib><creatorcontrib>Chen, David</creatorcontrib><creatorcontrib>Husic, Mia</creatorcontrib><creatorcontrib>Shooshtari, Parisa</creatorcontrib><title>TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, and its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to collect and present related TME data in an easily accessible format.
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| subjects | Analysis Breast cancer Cancer Colorectal cancer Data collection Datasets Diagnosis Digital archives Fibroblasts Gastric cancer Gene expression Gene Expression Profiling Gene sequencing Genetic aspects Head & neck cancer Medical research Medicine and Health Sciences Metadata Microenvironments Online data bases Prostate cancer RNA Sequence Analysis, RNA Single-Cell Analysis Software Throat cancer Tumor microenvironment Tumor Microenvironment - genetics Tumors |
| title | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool |
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