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PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, Aalt D. J. van Dijk
2011 Nucleic Acids Research  
Submitted datasets and results can be made publicly available through PRI-CAT, a feature that will enable community-based integrative analysis and visualization of ChIP-seq experiments.  ...  Secondary analysis of data can be performed with the aid of GALAXY, an external framework for tool and data integration. PRI-CAT is freely available at  ...  ACKNOWLEDGEMENTS We thank Jan van Haarst, Henri van de Geest and Bas te Lintel Hekkert for technical support and Dr Hailiang Mei for advice regarding GALAXY.  ... 
doi:10.1093/nar/gkr373 pmid:21609962 pmcid:PMC3125775 fatcat:4alzcmuc7ne27iwrt2l6mx3oby

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Li Chen, George Wu, Hongkai Ji
2011 Computer applications in the biosciences : CABIOS  
hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse.  ...  Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein-DNA interactions.  ...  Our ultimate goal is to turn it into a toolbox for biologists to efficiently integrate publicly available ChIP-chip and ChIP-seq data to study gene regulation and make novel discoveries.  ... 
doi:10.1093/bioinformatics/btr156 pmid:21450710 pmcid:PMC3087956 fatcat:vhvcvtpt3faxtncgbiqyspzesi

CistromeFinder for ChIP-seq and DNase-seq data reuse

H. Sun, B. Qin, T. Liu, Q. Wang, J. Liu, J. Wang, X. Lin, Y. Yang, L. Taing, P. K. Rao, M. Brown, Y. Zhang (+2 others)
2013 Bioinformatics  
CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets.  ...  It also allows users to leave comments to facilitate data evaluation and update. Availability: http://cistrome.org/finder. Contact:  ...  Most ChIP-seq and DNase-seq studies have raw data available from public repositories, such as NCBI Sequence Read Archive.  ... 
doi:10.1093/bioinformatics/btt135 pmid:23508969 pmcid:PMC3654708 fatcat:pe657u2x7jhmncwnvcdjfvemwq

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

Manuel Sánchez-Castillo, David Ruau, Adam C. Wilkinson, Felicia S.L. Ng, Rebecca Hannah, Evangelia Diamanti, Patrick Lombard, Nicola K. Wilson, Berthold Gottgens
2014 Nucleic Acids Research  
CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context  ...  CODEX (http://codex.stemcells.cam.ac.uk/) is a userfriendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental  ...  CODEX provides users with immediate access to uniformly analysed publicly available TF ChIP-Seq, histone ChIP-Seq, DNase-Seq and RNA-Seq experiments.  ... 
doi:10.1093/nar/gku895 pmid:25270877 pmcid:PMC4384009 fatcat:bno7pk57rbf7nnmlln4ktuvhb4

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data

Yingying Cao, Simo Kitanovski, Daniel Hoffmann
2020 BMC Genomics  
Results Here we introduce intePareto, a computational tool for the integrative analysis of RNA-Seq and ChIP-Seq data.  ...  As more and more biological samples are analyzed by the combination of ChIP-Seq and RNA-Seq, the integrated analysis of the corresponding data sets becomes, theoretically, a unique option to study gene  ...  About this supplement This article has been published as part of BMC Genomics Volume 21 Supplement 11 2020: Bioinformatics methods for biomedical data science.  ... 
doi:10.1186/s12864-020-07205-6 pmid:33372591 fatcat:qphhumhlufcy5lqsqnhxchgq6u

Cistrome: an integrative platform for transcriptional regulation studies

Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger (+5 others)
2011 Genome Biology  
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms.  ...  Cistrome is available at  ...  We thank Lingling Shen, Wenbo Wang, Jacqueline Wentz, Josiah Altschuler and Kar Joon Chew for their contributions to the system implementation.  ... 
doi:10.1186/gb-2011-12-8-r83 pmid:21859476 pmcid:PMC3245621 fatcat:25h6ewu5jrax3kxcvchynlx24e

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data

Christopher A. Lavender, Andrew J. Shapiro, Adam B. Burkholder, Brian D. Bennett, Karen Adelman, David C. Fargo
2017 Nucleic Acids Research  
However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques.  ...  Here, we present Online Resource for Integrative Omics (ORIO; https: //orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data.  ...  We thank Paul Wade, Guang Hu, and Jason Li for critical comments during review of the manuscript.  ... 
doi:10.1093/nar/gkx270 pmid:28402545 pmcid:PMC5449597 fatcat:7sn7bqiqkbdvvbgoyexr2v2mfi

Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data

Delasa Aghamirzaie, Karthik Raja Velmurugan, Shuchi Wu, Doaa Altarawy, Lenwood S. Heath, Ruth Grene
2017 F1000Research  
Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets.  ...  We present Expresso (database and webserver) as a tool for the Results: collection and integration of available ChIP-Seq peak data, which Arabidopsis in turn can be linked to a user's gene expression data  ...  David Bevan, for providing the opportunity to work on this project.  ... 
doi:10.12688/f1000research.10041.1 pmid:28529706 pmcid:PMC5414811 fatcat:rz6eikl4yzhgbm2exhzdzdyjlu

RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data

Miriam Rubio-Camarillo, Hugo López-Fernández, Gonzalo Gómez-López, Ángel Carro, José María Fernández, Coral Fustero Torre, Florentino Fdez-Riverola, Daniel Glez-Peña
2017 Computer Methods and Programs in Biomedicine  
and Objective: To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines  ...  bisulfite-seq and ChIP-seq experiments.  ...  SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure.  ... 
doi:10.1016/j.cmpb.2016.10.008 pmid:27886717 fatcat:dtoon7uu3bc7zbmgvbaqrmwiui

ImmuneRegulation: a web-based tool for identifying human immune regulatory elements

2019 Nucleic Acids Research  
from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations.  ...  on gene expression in multiple studies to empower investigators in translating these rich data into biological insights and clinical applications, and is freely available at https://immuneregulation.mssm.edu  ...  This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. FUNDING  ... 
doi:10.1093/nar/gkz450 pmid:31114925 pmcid:PMC6602512 fatcat:npkxyl4e75fcldu2aqtvqylcau

Nuclear EGFR and Integrator/Super Elongation Complex concurrently binds to Immediate Early Genes for gene transactivation

Victor Chun-Lam Wong
2018 Journal of Cancer  
By analyzing publicly available ChIP-seq and RNA-seq data, we aims to 1) explore the function of nEGFR, 2) unravel nEGFR target genes, and 3) discuss potential mechanisms of nEGFR chromatin recruitment  ...  In this study, we integrated gatekeepers of productive transcriptional elongation such as Integrator and Super Elongation Complex (SEC) to interrogate the function of nEGFR.  ...  In this study, we integrated collections of ChIP-seq, RNA-seq, and TCGA data publicly available to estimate the function of nEGFR, identify the nEGFR target genes, and exploring the clinical relevance  ... 
doi:10.7150/jca.21925 pmid:29290775 pmcid:PMC5743717 fatcat:6nq44kvdyrbzhljnaflsvpz5p4

A comprehensive resource for retrieving, visualizing, and integrating functional genomics data

Matthias Blum, Pierre-Etienne Cholley, Valeriya Malysheva, Samuel Nicaise, Julien Moehlin, Hinrich Gronemeyer, Marco Antonio Mendoza-Parra
2019 Life Science Alliance  
global or focused multidimensional data integration.  ...  However, in practice, interrogating large collections of public data requires major efforts for (i) reprocessing available raw reads, (ii) incorporating quality assessments to exclude artefactual and low-quality  ...  and maintenance of the required computational devices.  ... 
doi:10.26508/lsa.201900546 pmid:31818883 pmcid:PMC6907391 fatcat:hpqyu2qqqvfwxnbvjb4cx75heq

An integrated ChIP-seq analysis platform with customizable workflows

Eugenia G Giannopoulou, Olivier Elemento
2011 BMC Bioinformatics  
Although several programs have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually not well suited for thorough, integrative analysis of the detected  ...  Conclusions: ChIPseeqer facilitates ChIP-seq data analysis by offering a flexible and powerful set of computational tools that can be used in combination with one another.  ...  Kemerlis, for their suggestions in the revision of this manuscript.  ... 
doi:10.1186/1471-2105-12-277 pmid:21736739 pmcid:PMC3145611 fatcat:b566plvi35hjhprw3evdqx2gjy

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis

Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby
2019 F1000Research  
This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing  ...  of public RNA-Seq and ChIP-Seq data.  ...  We would also like to thank the Intramural Research Program of the National Library of Medicine for supporting this work.  ... 
doi:10.12688/f1000research.14880.3 fatcat:iqpkzhtr65bcfguohot4nosu5m

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

Julien Richard Albert, Tasuku Koike, Hamid Younesy, Richard Thompson, Aaron B. Bogutz, Mohammad M. Karimi, Matthew C. Lorincz
2018 BMC Genomics  
We validate allele-specific DNAme at known differentially methylated regions and show that automated integration of such methylation data with RNA-and ChIP-seq datasets yields an intuitive, multidimensional  ...  genes, highlighting MEA's utility for integrating human datasets of distinct provenance for genome-wide analysis of allelic phenomena.  ...  Availability of data and materials The datasets analyzed in this study are available in the Gene Expression Omnibus (GEO) and DNA Data Bank of Japan (DDBJ) repositories under codes: GSM1386023, GSM1845274  ... 
doi:10.1186/s12864-018-4835-2 pmid:29907088 pmcid:PMC6003194 fatcat:gibc7pblk5hilptzep6mezubne
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