iDREM: Interactive visualization of dynamic regulatory networks.
The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biolog...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-03-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006019&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849228203182260224 |
|---|---|
| author | Jun Ding James S Hagood Namasivayam Ambalavanan Naftali Kaminski Ziv Bar-Joseph |
| author_facet | Jun Ding James S Hagood Namasivayam Ambalavanan Naftali Kaminski Ziv Bar-Joseph |
| author_sort | Jun Ding |
| collection | DOAJ |
| description | The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs. |
| format | Article |
| id | doaj-art-19a10b93846f42d99eed04c13f45fbf5 |
| institution | Kabale University |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2018-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-19a10b93846f42d99eed04c13f45fbf52025-08-23T05:31:14ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582018-03-01143e100601910.1371/journal.pcbi.1006019iDREM: Interactive visualization of dynamic regulatory networks.Jun DingJames S HagoodNamasivayam AmbalavananNaftali KaminskiZiv Bar-JosephThe Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006019&type=printable |
| spellingShingle | Jun Ding James S Hagood Namasivayam Ambalavanan Naftali Kaminski Ziv Bar-Joseph iDREM: Interactive visualization of dynamic regulatory networks. PLoS Computational Biology |
| title | iDREM: Interactive visualization of dynamic regulatory networks. |
| title_full | iDREM: Interactive visualization of dynamic regulatory networks. |
| title_fullStr | iDREM: Interactive visualization of dynamic regulatory networks. |
| title_full_unstemmed | iDREM: Interactive visualization of dynamic regulatory networks. |
| title_short | iDREM: Interactive visualization of dynamic regulatory networks. |
| title_sort | idrem interactive visualization of dynamic regulatory networks |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006019&type=printable |
| work_keys_str_mv | AT junding idreminteractivevisualizationofdynamicregulatorynetworks AT jamesshagood idreminteractivevisualizationofdynamicregulatorynetworks AT namasivayamambalavanan idreminteractivevisualizationofdynamicregulatorynetworks AT naftalikaminski idreminteractivevisualizationofdynamicregulatorynetworks AT zivbarjoseph idreminteractivevisualizationofdynamicregulatorynetworks |