C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search
Abstract Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets re...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2017-09-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1786-6 |
| _version_ | 1818033127326482432 |
|---|---|
| author | Divya Tej Sowpati Surabhi Srivastava Jyotsna Dhawan Rakesh K Mishra |
| author_facet | Divya Tej Sowpati Surabhi Srivastava Jyotsna Dhawan Rakesh K Mishra |
| author_sort | Divya Tej Sowpati |
| collection | DOAJ |
| description | Abstract Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. Results We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. Conclusions C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles. |
| first_indexed | 2024-12-10T06:18:19Z |
| format | Article |
| id | doaj.art-99a44ab86e5b4a49ae314934bc9d815b |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T06:18:19Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-99a44ab86e5b4a49ae314934bc9d815b2022-12-22T01:59:24ZengBMCBMC Bioinformatics1471-21052017-09-0118S10132410.1186/s12859-017-1786-6C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern searchDivya Tej Sowpati0Surabhi Srivastava1Jyotsna Dhawan2Rakesh K Mishra3CSIR- Centre for Cellular and Molecular BiologyCSIR- Centre for Cellular and Molecular BiologyCSIR- Centre for Cellular and Molecular BiologyCSIR- Centre for Cellular and Molecular BiologyAbstract Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. Results We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. Conclusions C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles.http://link.springer.com/article/10.1186/s12859-017-1786-6Epigenetic patternsChromatin stateVisualizationJavaScriptGenome browserWeb app |
| spellingShingle | Divya Tej Sowpati Surabhi Srivastava Jyotsna Dhawan Rakesh K Mishra C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search BMC Bioinformatics Epigenetic patterns Chromatin state Visualization JavaScript Genome browser Web app |
| title | C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search |
| title_full | C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search |
| title_fullStr | C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search |
| title_full_unstemmed | C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search |
| title_short | C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search |
| title_sort | c state an interactive web app for simultaneous multi gene visualization and comparative epigenetic pattern search |
| topic | Epigenetic patterns Chromatin state Visualization JavaScript Genome browser Web app |
| url | http://link.springer.com/article/10.1186/s12859-017-1786-6 |
| work_keys_str_mv | AT divyatejsowpati cstateaninteractivewebappforsimultaneousmultigenevisualizationandcomparativeepigeneticpatternsearch AT surabhisrivastava cstateaninteractivewebappforsimultaneousmultigenevisualizationandcomparativeepigeneticpatternsearch AT jyotsnadhawan cstateaninteractivewebappforsimultaneousmultigenevisualizationandcomparativeepigeneticpatternsearch AT rakeshkmishra cstateaninteractivewebappforsimultaneousmultigenevisualizationandcomparativeepigeneticpatternsearch |