Exploring genomic datasets

Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. Methods: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play.

20p vioraclene 31-03-2024 4 2   Download

To explore the potential pathogenesis and clinical features of second primary glioblastoma (spGBM) follow‑ ing first primary renal cell carcinoma (fpRCC). Patients with spGBM after fpRCC were enrolled from our institution and the SEER dataset. Sanger sequencing, whole genome sequencing, and immunohistochemistry were used to detect molecular biomarkers.

8p vischultz 20-10-2023 7 1   Download

Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system.

10p vigalileogalilei 27-02-2022 13 1   Download

The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function.

23p vilichoo2711 23-06-2021 5 1   Download

Function of the immune system is correlated with the prognosis of the tumor. The effect of immune microenvironment on esophageal cancer (EC) development has not been fully investigated. This study aimed to explore a prognostic model based on immune-related genes (IRGs) for EC. We obtained the RNA-seq dataset and clinical information of EC from the Cancer Genome Atlas (TCGA).

16p vianrose2711 27-04-2021 6 2   Download

Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences of “batch” correction for biological discovery in two publicly available expression datasets.

10p vioklahoma2711 19-11-2020 7 2   Download

Computational biologists daily face the need to explore massive amounts of genomic data. New visualization techniques can help researchers navigate and understand these big data. Horizon Charts are a relatively new visualization method that, under the right circumstances, maximizes data density without losing graphical perception.

4p vioklahoma2711 19-11-2020 9 2   Download

Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research.

15p vicolorado2711 22-10-2020 16 0   Download

Omics-profiling is a collection of increasingly prominent approaches that result in large-scale biological datasets, for instance capturing an organism’s behavior and response in an environment. It can be daunting to manually analyze and interpret such large datasets without some programming experience.

8p vicolorado2711 22-10-2020 7 0   Download

Molecular genetic markers correspond to highly potent source for the study of plant genomes and the association of inherited phenotypic traits with underneath genetic variation. Single Nucleotide Polymorphism (SNPs) are most abundant form of molecular genetic marker which represents a single nucleotide difference between two individuals at a defined location. Compare to others SNPs are direct sequence variation which offers the precise nature of the allelic variants among different genotypes. Further, it signify recurrent type of genetic polymorphism with high density genome coverage.

11p nguaconbaynhay1 04-12-2019 26 0   Download