FungiDB 34 Released

Update from EuPathDB:

We are pleased to announce the release of FungiDB 34

New data in this release
Genome Sequence and Annotation: these annotated genomes appear for the first time in FungiDB.
·        Clavispora lusitaniae ATCC 42720 – Butler G et al.
·        Magnaporthe oryzae BR32 – Chiapello et al.
·        Uncinocarpus reesii 1704 – Sharpton et al.
·        Zymoseptoria tritici IPO323 – Grandaubert et al. and Goodwin et al.

RNA Sequencing data
·        Characterization of light regulated genes – Wu et al.
·        Transcriptome of Magnaporthe oryzae isolates collected from Bangladeshi fields – Islam et al.
·        Transcriptome of Magnaporthe oryzae isolates collected from Bangladeshi fields (aligned to BR32) – Islam et al.
·        The Cryptococcus neoformans transcriptome at the site of human meningitis (paired-end data) – Chen et al.
·        The Cryptococcus neoformans transcriptome at the site of human meningitis (single-read data) – Chen et al.

Proteomics data
·        Phosphoproteome in non-limiting conditions – Fusarium graminearum phosphoproteome in non-limiting conditions. Rampitsch et al.

Chip-seq data
·        ADV-1 gene targets ChIP-seq – ADV-1 functions to generate distinct temporal dynamics of target genes in Neurospora crassa. Dekhang et al.


Neurospora crassa e-Compendium
PubMed IDs from Neurospora crassa e-Compendium by Alan Radford and Matt Sachs have been loaded for Neurospora crassa OR74A. The list of loaded publications is available.


New features in this release

REVIGO direct link
EuPathDB now offers a direct link from gene ontology (GO) enrichment results to REVIGO, a tool that provides GO term summarization and visualization. To access this feature first run a GO term enrichment using the 'Analyze Results' option from any gene search result. Then click on the 'Start Revigo Analysis' link (upper right hand side of enrichment results) to populate the REVIGO submission page with your GO enrichment results from EuPathDB. Follow instructions on the REVIGO page to complete your analysis.

External database links
·        In a collaborative effort between FungiDB and PHI-Base, FungiDB gene pages now contain links to PHI-Base for 47 fungal organisms.
·        In a collaborative effort between FungiDB and JGI, FungiDB Aspergillus nidulans gene pages now contain links to JGI record pages.
 
Interpreting RNA Seq data on FungiDB
         
     Gene page expression graphs as well as all GBrowse coverage plots display data from uniquely aligned reads, which align to one location only.  This may under-represent expression for genes that are duplicated in the genome. See this news item to learn more about how to view non-unique reads and improvements planned for future releases.

As always, Contact Us with questions or concerns.

Sincerely,

The EuPathDB Team

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