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Analysis of Pan-omics Data in Human Interactome Network (APODHIN)
Analysis of Pan-omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-inte...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753071/ https://www.ncbi.nlm.nih.gov/pubmed/33363571 http://dx.doi.org/10.3389/fgene.2020.589231 |
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author | Biswas, Nupur Kumar, Krishna Bose, Sarpita Bera, Raisa Chakrabarti, Saikat |
author_facet | Biswas, Nupur Kumar, Krishna Bose, Sarpita Bera, Raisa Chakrabarti, Saikat |
author_sort | Biswas, Nupur |
collection | PubMed |
description | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-interactome network consisting of human protein–protein interactions (PPIs), miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships. In its first module, APODHIN maps proteins/genes/miRNAs from different omics data in its meta-interactome network and extracts the network of biomolecules that are differentially altered in the given scenario. Using this context specific, filtered interaction network, APODHIN identifies topologically important nodes (TINs) implementing graph theory based network topology analysis and further justifies their role via pathway and disease marker mapping. These TINs could be used as prospective diagnostic and/or prognostic biomarkers and/or potential therapeutic targets. In its second module, APODHIN attempts to identify cross pathway regulatory and PPI links connecting signaling proteins, transcription factors (TFs), and miRNAs to metabolic enzymes via utilization of single-omics and/or pan-omics data and implementation of mathematical modeling. Interconnections between regulatory components such as signaling proteins/TFs/miRNAs and metabolic pathways need to be elucidated more elaborately in order to understand the role of oncogene and tumor suppressors in regulation of metabolic reprogramming during cancer. APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links. Tabular, graphical and 3D network representations of the identified TINs and cross-pathway links are provided for better appreciation. Additionally, this platform also provides few example data analysis of cancer specific, single and/or multi omics dataset for cervical, ovarian, and breast cancers where meta-interactome networks, TINs, and cross-pathway links are provided. APODHIN platform is freely available at http://www.hpppi.iicb.res.in/APODHIN/home.html. |
format | Online Article Text |
id | pubmed-7753071 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-77530712020-12-23 Analysis of Pan-omics Data in Human Interactome Network (APODHIN) Biswas, Nupur Kumar, Krishna Bose, Sarpita Bera, Raisa Chakrabarti, Saikat Front Genet Genetics Analysis of Pan-omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-interactome network consisting of human protein–protein interactions (PPIs), miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships. In its first module, APODHIN maps proteins/genes/miRNAs from different omics data in its meta-interactome network and extracts the network of biomolecules that are differentially altered in the given scenario. Using this context specific, filtered interaction network, APODHIN identifies topologically important nodes (TINs) implementing graph theory based network topology analysis and further justifies their role via pathway and disease marker mapping. These TINs could be used as prospective diagnostic and/or prognostic biomarkers and/or potential therapeutic targets. In its second module, APODHIN attempts to identify cross pathway regulatory and PPI links connecting signaling proteins, transcription factors (TFs), and miRNAs to metabolic enzymes via utilization of single-omics and/or pan-omics data and implementation of mathematical modeling. Interconnections between regulatory components such as signaling proteins/TFs/miRNAs and metabolic pathways need to be elucidated more elaborately in order to understand the role of oncogene and tumor suppressors in regulation of metabolic reprogramming during cancer. APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links. Tabular, graphical and 3D network representations of the identified TINs and cross-pathway links are provided for better appreciation. Additionally, this platform also provides few example data analysis of cancer specific, single and/or multi omics dataset for cervical, ovarian, and breast cancers where meta-interactome networks, TINs, and cross-pathway links are provided. APODHIN platform is freely available at http://www.hpppi.iicb.res.in/APODHIN/home.html. Frontiers Media S.A. 2020-12-08 /pmc/articles/PMC7753071/ /pubmed/33363571 http://dx.doi.org/10.3389/fgene.2020.589231 Text en Copyright © 2020 Biswas, Kumar, Bose, Bera and Chakrabarti. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Biswas, Nupur Kumar, Krishna Bose, Sarpita Bera, Raisa Chakrabarti, Saikat Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title_full | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title_fullStr | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title_full_unstemmed | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title_short | Analysis of Pan-omics Data in Human Interactome Network (APODHIN) |
title_sort | analysis of pan-omics data in human interactome network (apodhin) |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753071/ https://www.ncbi.nlm.nih.gov/pubmed/33363571 http://dx.doi.org/10.3389/fgene.2020.589231 |
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