Interferome v2.0: an updated database of annotated interferon-regulated genes

Irina Rusinova, Samuel Forster, Simon Xiaoming Yu, Anitha Kannan, Marion Masse, Helen Elizabeth Cumming, Ross Chapman, Paul John Hertzog

Research output: Contribution to journalArticleResearchpeer-review

269 Citations (Scopus)

Abstract

Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.
Original languageEnglish
Pages (from-to)D1040-D1046
Number of pages7
JournalNucleic Acids Research
Volume41
Issue numberD1
DOIs
Publication statusPublished - 2013

Cite this

Rusinova, Irina ; Forster, Samuel ; Yu, Simon Xiaoming ; Kannan, Anitha ; Masse, Marion ; Cumming, Helen Elizabeth ; Chapman, Ross ; Hertzog, Paul John. / Interferome v2.0: an updated database of annotated interferon-regulated genes. In: Nucleic Acids Research. 2013 ; Vol. 41, No. D1. pp. D1040-D1046.
@article{26fd6ab8e0e4492f99c8a2d062efb1c8,
title = "Interferome v2.0: an updated database of annotated interferon-regulated genes",
abstract = "Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.",
author = "Irina Rusinova and Samuel Forster and Yu, {Simon Xiaoming} and Anitha Kannan and Marion Masse and Cumming, {Helen Elizabeth} and Ross Chapman and Hertzog, {Paul John}",
year = "2013",
doi = "10.1093/nar/gks1215",
language = "English",
volume = "41",
pages = "D1040--D1046",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

Rusinova, I, Forster, S, Yu, SX, Kannan, A, Masse, M, Cumming, HE, Chapman, R & Hertzog, PJ 2013, 'Interferome v2.0: an updated database of annotated interferon-regulated genes', Nucleic Acids Research, vol. 41, no. D1, pp. D1040-D1046. https://doi.org/10.1093/nar/gks1215

Interferome v2.0: an updated database of annotated interferon-regulated genes. / Rusinova, Irina; Forster, Samuel; Yu, Simon Xiaoming; Kannan, Anitha; Masse, Marion; Cumming, Helen Elizabeth; Chapman, Ross; Hertzog, Paul John.

In: Nucleic Acids Research, Vol. 41, No. D1, 2013, p. D1040-D1046.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Interferome v2.0: an updated database of annotated interferon-regulated genes

AU - Rusinova, Irina

AU - Forster, Samuel

AU - Yu, Simon Xiaoming

AU - Kannan, Anitha

AU - Masse, Marion

AU - Cumming, Helen Elizabeth

AU - Chapman, Ross

AU - Hertzog, Paul John

PY - 2013

Y1 - 2013

N2 - Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.

AB - Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.

UR - http://nar.oxfordjournals.org/content/41/D1/D1040.full.pdf

U2 - 10.1093/nar/gks1215

DO - 10.1093/nar/gks1215

M3 - Article

VL - 41

SP - D1040-D1046

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -