31 research outputs found
Discriminative Topological Features Reveal Biological Network Mechanisms
Recent genomic and bioinformatic advances have motivated the development of
numerous random network models purporting to describe graphs of biological,
technological, and sociological origin. The success of a model has been
evaluated by how well it reproduces a few key features of the real-world data,
such as degree distributions, mean geodesic lengths, and clustering
coefficients. Often pairs of models can reproduce these features with
indistinguishable fidelity despite being generated by vastly different
mechanisms. In such cases, these few target features are insufficient to
distinguish which of the different models best describes real world networks of
interest; moreover, it is not clear a priori that any of the presently-existing
algorithms for network generation offers a predictive description of the
networks inspiring them. To derive discriminative classifiers, we construct a
mapping from the set of all graphs to a high-dimensional (in principle
infinite-dimensional) ``word space.'' This map defines an input space for
classification schemes which allow us for the first time to state unambiguously
which models are most descriptive of the networks they purport to describe. Our
training sets include networks generated from 17 models either drawn from the
literature or introduced in this work, source code for which is freely
available. We anticipate that this new approach to network analysis will be of
broad impact to a number of communities.Comment: supplemental website:
http://www.columbia.edu/itc/applied/wiggins/netclass
Geoseq: a tool for dissecting deep-sequencing datasets
Gurtowski J, Cancio A, Shah H, et al. Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics. 2010;11(1): 506.Background
Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest.
Results
Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment.
Conclusions
Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a) identify differential isoform expression in mRNA-seq datasets, b) identify miRNAs (microRNAs) in libraries, and identify mature and star sequences in miRNAS and c) to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool
Biomarkers in anal cancer: from biological understanding to stratified treatment
Squamous cell carcinomas of the anus and anal canal represent a model of a cancer and perhaps the first where level 1 evidence supported primary chemoradiotherapy (CRT) in treating locoregional disease with curative intent. The majority of tumours are associated with infection with oncogenic subtypes of human papilloma virus and this plays a significant role in their sensitivity to treatment. However, not all tumours are cured with CRT and there remain opportunities to improve outcomes in terms of oncological control and also reducing late toxicities. Understanding the biology of ASCC promises to allow a more personalised approach to treatment, with the development and validation of a range of biomarkers and associated techniques that are the focus of this review
Tgf ß receptor 1: An immune susceptibility gene in hpv-associated cancer
Only a minority of those exposed to human papillomavirus (HPV) develop HPV-related cervical and oropharyngeal cancer. Because host immunity affects infection and progression to cancer, we tested the hypothesis that genetic variation in immune-related genes is a determinant of susceptibility to oropharyngeal cancer and other HPV-associated cancers by performing a multitier integrative computational analysis with oropharyngeal cancer data from a head and neck cancer genome-wide association study (GWAS). Independent analyses, including single-gene, gene-interconnectivity, protein-protein interaction, gene expression, and pathway analysis, identified immune genes and pathways significantly associated with oropharyngeal cancer. TGFßR1, which intersected all tiers of analysis and thus selected for validation, replicated significantly in the head and neck cancer GWAS limited to HPV-seropositive cases and an independent cervical cancer GWAS. The TGFbR1 containing p38-MAPK pathway was significantly associated with oropharyngeal cancer and cervical cancer, and TGFßR1 was overexpressed in oropharyngeal cancer, cervical cancer, andHPV+ head and neck cancer tumors. These concordant analyses implicate TGFßR1 signaling as a process dysregulated across HPV-related cancers. This study demonstrates that genetic variation in immune-related genes is associated with susceptibility to oropharyngeal cancer and implicates TGF ßR1/TGFß signaling in the development of both oropharyngeal cancer and cervical cancer. Better understanding of the immunogenetic basis of susceptibility to HPV-associated cancers may provide insight into host/virus interactions and immune processes dysregulated in the minority of HPV-exposed individuals who progress to cancer. © 2014 American Association for Cancer Research