A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification
<p dir="ltr">The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field...
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2018
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| _version_ | 1864513510853050368 |
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| author | Jessica Roelands (7516439) |
| author2 | Julie Decock (44558) Sabri Boughorbel (846228) Darawan Rinchai (742366) Cristina Maccalli (2632465) Michele Ceccarelli (184154) Michael Black (246211) Cris Print (5980712) Jeff Chou (69693) Scott Presnell (18891829) Charlie Quinn (18891832) Puthen Jithesh (6561377) Najeeb Syed (12561967) Salha B.J. Al Bader (18891835) Shahinaz Bedri (4480651) Ena Wang (802) Francesco M. Marincola (8823902) Damien Chaussabel (26369) Peter Kuppen (3853129) Lance D. Miller (8444226) Davide Bedognetti (2632474) Wouter Hendrickx (44559) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Jessica Roelands (7516439) Julie Decock (44558) Sabri Boughorbel (846228) Darawan Rinchai (742366) Cristina Maccalli (2632465) Michele Ceccarelli (184154) Michael Black (246211) Cris Print (5980712) Jeff Chou (69693) Scott Presnell (18891829) Charlie Quinn (18891832) Puthen Jithesh (6561377) Najeeb Syed (12561967) Salha B.J. Al Bader (18891835) Shahinaz Bedri (4480651) Ena Wang (802) Francesco M. Marincola (8823902) Damien Chaussabel (26369) Peter Kuppen (3853129) Lance D. Miller (8444226) Davide Bedognetti (2632474) Wouter Hendrickx (44559) |
| author_role | author |
| dc.creator.none.fl_str_mv | Jessica Roelands (7516439) Julie Decock (44558) Sabri Boughorbel (846228) Darawan Rinchai (742366) Cristina Maccalli (2632465) Michele Ceccarelli (184154) Michael Black (246211) Cris Print (5980712) Jeff Chou (69693) Scott Presnell (18891829) Charlie Quinn (18891832) Puthen Jithesh (6561377) Najeeb Syed (12561967) Salha B.J. Al Bader (18891835) Shahinaz Bedri (4480651) Ena Wang (802) Francesco M. Marincola (8823902) Damien Chaussabel (26369) Peter Kuppen (3853129) Lance D. Miller (8444226) Davide Bedognetti (2632474) Wouter Hendrickx (44559) |
| dc.date.none.fl_str_mv | 2018-02-09T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.12688/f1000research.10960.2 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/A_collection_of_annotated_and_harmonized_human_breast_cancer_transcriptome_datasets_including_immunologic_classification/26114629 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology Oncology and carcinogenesis Breast Cancer Immune Subtypes Cancer Immune Phenotype Gene Expression Browser Immunologic Constant of Rejection |
| dc.title.none.fl_str_mv | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at: <a href="http://breastcancer.gxbsidra.org/dm3/geneBrowser/list" rel="noreferrer" target="_blank">http://breastcancer.gxbsidra.org/dm3/geneBrowser/list</a>.</p><h2>Other Information</h2><p dir="ltr">Published in: F1000Research<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.12688/f1000research.10960.2" target="_blank">https://dx.doi.org/10.12688/f1000research.10960.2</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_4a65fd6024b9514b67a19e2725972f93 |
| identifier_str_mv | 10.12688/f1000research.10960.2 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26114629 |
| publishDate | 2018 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classificationJessica Roelands (7516439)Julie Decock (44558)Sabri Boughorbel (846228)Darawan Rinchai (742366)Cristina Maccalli (2632465)Michele Ceccarelli (184154)Michael Black (246211)Cris Print (5980712)Jeff Chou (69693)Scott Presnell (18891829)Charlie Quinn (18891832)Puthen Jithesh (6561377)Najeeb Syed (12561967)Salha B.J. Al Bader (18891835)Shahinaz Bedri (4480651)Ena Wang (802)Francesco M. Marincola (8823902)Damien Chaussabel (26369)Peter Kuppen (3853129)Lance D. Miller (8444226)Davide Bedognetti (2632474)Wouter Hendrickx (44559)Biological sciencesGeneticsBiomedical and clinical sciencesClinical sciencesImmunologyOncology and carcinogenesisBreast CancerImmune SubtypesCancer Immune PhenotypeGene Expression BrowserImmunologic Constant of Rejection<p dir="ltr">The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at: <a href="http://breastcancer.gxbsidra.org/dm3/geneBrowser/list" rel="noreferrer" target="_blank">http://breastcancer.gxbsidra.org/dm3/geneBrowser/list</a>.</p><h2>Other Information</h2><p dir="ltr">Published in: F1000Research<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.12688/f1000research.10960.2" target="_blank">https://dx.doi.org/10.12688/f1000research.10960.2</a></p>2018-02-09T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.12688/f1000research.10960.2https://figshare.com/articles/journal_contribution/A_collection_of_annotated_and_harmonized_human_breast_cancer_transcriptome_datasets_including_immunologic_classification/26114629CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/261146292018-02-09T03:00:00Z |
| spellingShingle | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification Jessica Roelands (7516439) Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology Oncology and carcinogenesis Breast Cancer Immune Subtypes Cancer Immune Phenotype Gene Expression Browser Immunologic Constant of Rejection |
| status_str | publishedVersion |
| title | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| title_full | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| title_fullStr | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| title_full_unstemmed | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| title_short | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| title_sort | A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification |
| topic | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Immunology Oncology and carcinogenesis Breast Cancer Immune Subtypes Cancer Immune Phenotype Gene Expression Browser Immunologic Constant of Rejection |