CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms

Nucleic Acids Research
George S KrasnovAnna V Kudryavtseva

Abstract

The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA-miRNA and gene-transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF-gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource. Similarly, CrossHub identifies mRNA-miRNA pairs with predicted or validated binding sites (TargetScan, mirSVR, PicTar, DIANA microT, miRTarBase) and strong negative expression correlations. We observed partial consistency between ChIP-Seq or miRNA target predictions and gene-TF/miRNA co-expression, demonstrating a link between these indicators. Additionally, CrossHub expression-methylation correlation analysis can be used to identify hypermethylated CpG sites or regions with the greatest potential impact on gene expression. Thus, CrossHub is capable of outlining molecular po...Continue Reading

References

Apr 5, 2005·Nature Genetics·Azra KrekNikolaus Rajewsky
Jun 27, 2007·RNA·George EasowStephen M Cohen
Jul 20, 2007·RNA Biology·Michaela BeitzingerGunter Meister
Oct 19, 2007·Nucleic Acids Research·Seungyoon NamSanghyuk Lee
Oct 29, 2008·Genome Research·Robin C FriedmanDavid P Bartel
Nov 8, 2008·Bioinformatics·Adi Laurentiu TarcaRoberto Romero
May 2, 2009·Nucleic Acids Research·M MaragkakisA G Hatzigeorgiou
Oct 29, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Chi V DangPing Gao
Apr 14, 2010·Molecular Cell·John S TsangAlexander van Oudenaarden
Apr 29, 2011·PLoS Biology·UNKNOWN ENCODE Project Consortium
May 25, 2011·Journal of Biomedical Informatics·Harsh DweepNorbert Gretz
May 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Grzegorz KudlaDavid Tollervey
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 7, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Giorgia MigliardiAndrea Bertotti
Apr 3, 2012·Cell·Chi V Dang
Apr 12, 2012·Epigenetics : Official Journal of the DNA Methylation Society·Alexey A DmitrievEugene R Zabarovsky
May 9, 2012·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Rainer ClausJohn C Byrd
Jun 12, 2012·Genome Research·Andrea SmallwoodBing Ren
Jul 20, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Aug 29, 2012·Methods : a Companion to Methods in Enzymology·Markus HafnerDoron Betel
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Nov 30, 2012·Nucleic Acids Research·Sooyoung ChoSanghyuk Lee
Mar 1, 2013·Expert Opinion on Therapeutic Targets·George S KrasnovAnna V Kudryavtseva
Mar 13, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Vera N SenchenkoEugene R Zabarovsky
Jun 1, 2013·Genomics, Proteomics & Bioinformatics·Hongzhu Qu, Xiangdong Fang
Aug 30, 2013·Expert Opinion on Therapeutic Targets·George S KrasnovAnna V Kudryavtseva
Dec 29, 2013·Stem Cell Reports·Kohei YamamizuMinoru S H Ko

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Citations

Feb 1, 2018·Journal of Bioinformatics and Computational Biology·George S KrasnovAlexey A Dmitriev
Jan 3, 2018·Nucleic Acids Research·Gary Wilk, Rosemary Braun
Jun 13, 2020·Journal of Oral Pathology & Medicine : Official Publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology·Guangming ZhouBin Zhang
Jan 21, 2017·BMC Genomics·Anastasiya Vladimirovna SnezhkinaAnna Viktorovna Kudryavtseva
Jun 6, 2018·Frontiers in Genetics·Artemy D BeniaminovAlexey A Dmitriev
Mar 19, 2019·Frontiers in Genetics·George S KrasnovAlexey A Dmitriev
Jan 1, 2017·Molecular Biology·V M BlinovA V Shargunov
Apr 11, 2019·BMC Medical Genetics·Maria S FedorovaAnna V Kudryavtseva
Sep 11, 2018·Cancer Biomarkers : Section a of Disease Markers·Jianmin LiuYan Wang

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