PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data
Summary: Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TF...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-06-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723001612 |
| _version_ | 1797855301924290560 |
|---|---|
| author | Taiyun Kim Hani Jieun Kim Andrew J. Oldfield Pengyi Yang |
| author_facet | Taiyun Kim Hani Jieun Kim Andrew J. Oldfield Pengyi Yang |
| author_sort | Taiyun Kim |
| collection | DOAJ |
| description | Summary: Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TFs and chromatin-regulating proteins from mouse embryonic stem cells at various functional genomic regions. We describe steps for accessing and searching the PAD2 database and selecting and submitting genomic regions. We then detail protein colocalization analysis using heatmap and ranked correlation plot.For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-09T20:20:23Z |
| format | Article |
| id | doaj.art-f42c6b59aff84ea8913d6b123c743f70 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-09T20:20:23Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-f42c6b59aff84ea8913d6b123c743f702023-03-31T05:55:29ZengElsevierSTAR Protocols2666-16672023-06-0142102203PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq dataTaiyun Kim0Hani Jieun Kim1Andrew J. Oldfield2Pengyi Yang3Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia; Corresponding authorComputational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, AustraliaInstitut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, FranceComputational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia; Corresponding authorSummary: Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TFs and chromatin-regulating proteins from mouse embryonic stem cells at various functional genomic regions. We describe steps for accessing and searching the PAD2 database and selecting and submitting genomic regions. We then detail protein colocalization analysis using heatmap and ranked correlation plot.For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723001612BioinformaticsSequence AnalysisGenomicsStem CellsSystems Biology |
| spellingShingle | Taiyun Kim Hani Jieun Kim Andrew J. Oldfield Pengyi Yang PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data STAR Protocols Bioinformatics Sequence Analysis Genomics Stem Cells Systems Biology |
| title | PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data |
| title_full | PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data |
| title_fullStr | PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data |
| title_full_unstemmed | PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data |
| title_short | PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data |
| title_sort | pad2 interactive exploration of transcription factor genomic colocalization using chip seq data |
| topic | Bioinformatics Sequence Analysis Genomics Stem Cells Systems Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723001612 |
| work_keys_str_mv | AT taiyunkim pad2interactiveexplorationoftranscriptionfactorgenomiccolocalizationusingchipseqdata AT hanijieunkim pad2interactiveexplorationoftranscriptionfactorgenomiccolocalizationusingchipseqdata AT andrewjoldfield pad2interactiveexplorationoftranscriptionfactorgenomiccolocalizationusingchipseqdata AT pengyiyang pad2interactiveexplorationoftranscriptionfactorgenomiccolocalizationusingchipseqdata |