A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research

Darawan Rinchai, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Damien J. Chaussabel

Research output: Contribution to journalComment/debate

4 Citations (Scopus)

Abstract

Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.

Original languageEnglish
Article number291
JournalF1000Research
Volume5
DOIs
Publication statusPublished - 2016

Fingerprint

Transcriptome
Gene expression
Monocytes
Landing
Research
Data mining
Visualization
Genes
Gene Expression
Translational Medical Research
Research Personnel
Datasets

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

Cite this

@article{8ad53789f5f34427a89692590827ebe2,
title = "A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research",
abstract = "Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.",
author = "Darawan Rinchai and Sabri Boughorbel and Scott Presnell and Charlie Quinn and Chaussabel, {Damien J.}",
year = "2016",
doi = "10.12688/f1000research.8182.2",
language = "English",
volume = "5",
journal = "F1000Research",
issn = "2046-1402",
publisher = "F1000 Research Ltd.",

}

TY - JOUR

T1 - A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research

AU - Rinchai, Darawan

AU - Boughorbel, Sabri

AU - Presnell, Scott

AU - Quinn, Charlie

AU - Chaussabel, Damien J.

PY - 2016

Y1 - 2016

N2 - Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.

AB - Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.

UR - http://www.scopus.com/inward/record.url?scp=84978533704&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84978533704&partnerID=8YFLogxK

U2 - 10.12688/f1000research.8182.2

DO - 10.12688/f1000research.8182.2

M3 - Comment/debate

AN - SCOPUS:84978533704

VL - 5

JO - F1000Research

JF - F1000Research

SN - 2046-1402

M1 - 291

ER -