Title: HMP2 gut microbiota and IBD

Analysis pertains to to the public data provided by the study,"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome". In order to infer microbial (and inter-omic) association patterns in inflammatory bowel disease, taxonomic and functional profiles corresponding to the metagenomic study (downloadable from MetagenoNets demo page) were obtained from the Inflammatory Bowel Disease Multi'omics Database pertaining to HMP2 (https://ibdmdb.org/). We considered the zeroth day sample corresponding to all the subjects in the study (76 IBD – 48 CD, 28 UC; 24 nonIBD). Both taxonomic as well as functional profiles along with given metadata was utilized to create integrated/ microbial association networks using MetagenoNets.

DOI: https://doi.org/10.1038/s41564-017-0089-z

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Title: Tribal and urban gut microbiome data

Analysis pertains to the public data provided by the study, "Lifestyle-Induced Microbial Gradients: An Indian Perspective". Study considered 155 16S metagenomic samples collected from 75 tribal and 80 urban gut microbiome samples. Inferred function potential of the microbiota profiles of this study was used as secondary inter-omic data. Both taxonomic as well as functional profiles along with given metadata was utilized to create integrated/ microbial association networks using MetagenoNets.

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DOI: https://doi.org/10.3389/fmicb.2019.02874

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Title: IBD Gut and Tissue microbiome data

Analysis pertains to the public data provided by the study titled, "Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment". Study considered 228 16S metagenomic samples (stool and biopsy) collected from Ocean State Crohn's and Colitis Area Registry (OSCCAR) and the Prospective Registry in IBD Study at MGH (PRISM) database. Authors originally observed that "there were major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways". Both taxonomic as well as inferred functional profiles along with given metadata was utilized to create integrated/ microbial association networks using MetagenoNets.

DOI: https://doi.org/10.1186/gb-2012-13-9-r79

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Title: Hypertension gut microbiome data

Analysis pertains to the public data provided by the study, "Gut microbiota dysbiosis contributes to the development of hypertension". Authors performed shotgun metagenomic sequencing of fecal samples from a cohort of 196 Chinese individuals. In order to establish the role of gut microbiota dysbiosis as a key factor for blood pressure (BP) changes that triggers the pathogenesis of hypertension, they classified the cohort into 41 healthy controls, 56 pre-hypertension (pHTN), and 99 hypertension (HTN) samples according to their BP levels. We utilized the abundance data as well as metadata provided in this study. Only the differentiating set of genera reported by the authors were used to construct network using MetagenoNets for better clarity and reproducibility of results. Both taxonomic as well as functional profiles along with given metadata was utilized to create integrated/ microbial association networks using MetagenoNets.

DOI: https://doi.org/10.1186/s40168-016-0222-x

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