J-Circos: an interactive Circos plotter

An, Jiyuan; Lai, John; Sajjanhar, Atul; Batra, Jyotsna; Wang, Chenwei; Nelson, Colleen C.

doi:10.1093/bioinformatics/btu842

Cited by 62 publications

(40 citation statements)

References 8 publications

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“…Enrichr was used to test if particular chromosomal locations were enriched in the group of DEGs in NE-like vs. AdenoPCa samples [56]. J-Circos was used to perform circular plot with human chromosomes [57].…”

Section: Functional Analysismentioning

confidence: 99%

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma

Ostano

Mello-Grand

Sesia

et al. 2020

IJMS

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Neuroendocrine prostate cancer (NEPC) can arise de novo, but much more commonly occurs as a consequence of a selective pressure from androgen deprivation therapy or androgen receptor antagonists used for prostate cancer (PCa) treatment. The process is known as neuroendocrine transdifferentiation. There is little molecular characterization of NEPCs and consequently there is no standard treatment for this kind of tumors, characterized by highly metastases rates and poor survival. For this purpose, we profiled 54 PCa samples with more than 10-years follow-up for gene and miRNA expression. We divided samples into two groups (NE-like vs. AdenoPCa), according to their clinical and molecular features. NE-like tumors were characterized by a neuroendocrine fingerprint made of known neuroendocrine markers and novel molecules, including long non-coding RNAs and components of the estrogen receptor signaling. A gene expression signature able to predict NEPC was built and tested on independently published datasets. This study identified molecular features (protein-coding, long non-coding, and microRNAs), at the time of surgery, that may anticipate the NE transformation process of prostate adenocarcinoma. Our results may contribute to improving the diagnosis and treatment of this subgroup of tumors for which traditional therapy regimens do not show beneficial effects.

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Section: Functional Analysismentioning

confidence: 99%

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma

Ostano

Mello-Grand

Sesia

et al. 2020

IJMS

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“…SNVs were also independently called using Partek Genomics Suite and Varscan 2 . The Circos plot was generated using J‐Circos . The primary goal of the analysis was to identify somatic variants with high confidence, and determine which variants were in common or different in the 2 tumor samples.…”

Section: Methodsmentioning

confidence: 99%

Genomic analysis of melanoma evolution following a 30‐year disease‐free interval

et al. 2017

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Ultra-late melanoma recurrence is infrequent, poorly understood and, in most cases, difficult to unambiguously distinguish from a new primary melanoma. We identified a patient with a second melanoma diagnosed after a 30-year disease-free interval, and sought to determine if this new lesion was a recurrence of the original melanoma. Here we report the genomic sequence analysis of the exomes of 2 melanoma lesions isolated from the same individual in 1985 and 2015, and their comparison to each other and to the germline DNA of the patient. Identification of many shared somatic mutations between these lesions proves a lineal relationship spanning 30 years. Unlike prior reports of ultra-late melanoma recurrence, the availability of the original tumor and the use of comprehensive genomic analysis allowed us to confirm that the second lesion is truly a recurrence. We demonstrate the acquisition of numerous additional mutations during the 3 decade asymptomatic period. These data highlight the low but very long-lasting risk of recurrence in this patient population.

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“…We correlated the ONT sequencing data with the Illumina datasets as previously described [105] using the wub package (v.0.2) [106]. The genome coverage of sequencing datasets were generated using bedtools genome coverage (v2.27) [107] and visualised via J-Circos (v1) [108]. Log2-fold ratios were calculated using DeepTools bamCompare (v.2.5.1) [109].…”

Section: Mapping and Qualitative Analysismentioning

confidence: 99%

Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites

Lee

Judd

Jex

et al. 2020

Preprint

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Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AT content of Plasmodium RNA, but also the limitations of short read sequencing in deciphering complex splicing events. In this study, we utilised the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies (ONT) to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or near full-length transcripts with comparable quantification to Illumina sequencing. By comparing this data with available gene models, we find widespread alternative splicing, particular intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This work highlights a strategy in using long read sequencing to understand splicing events at the whole transcript level, and has implications in future interpretation of RNA-seq studies.

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J-Circos: an interactive Circos plotter

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 62 publications

References 8 publications

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma

Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma

Genomic analysis of melanoma evolution following a 30‐year disease‐free interval

Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites

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