Transcriptional Complexity of CERKL Gene

 
In order to analyze the transcriptional repertoire of CERKL in human and mouse, both computational and wet-lab experiments were conducted. The genomic sequences were explored to determine the promoters and the corresponding transcription start sites (TSSs), the alternative splicing variants, as well as the different putative translation initiation sites (TISs), which altogether is compatible with a wide display of functional domains and contributes to the final mRNA and protein complexity for this gene.

• Further details are available at the following reference:
      High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse
      Garanto, et al, IOVS, 2011, 52(8):5202.

Transcriptome Sequencing by 454

 
A detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. In order to obtain the most representative set of planarian genes expressed under different physiological conditions, total RNA was isolated from a mixture of non-irradiated and irradiated intact and regenerating planarians of species Schmidtea mediterranea . We have performed sequence analyses on the assemblies of reads obtained by 454-sequencing from that pool of transcripts. Among those analyses, functional annotation was useful in order to identify putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.

• Further details are available at the following reference:
      Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
      Abril, Cebrià, et al, BMC Genomics, 2010, 11:731.
• Data is available through the Smed454 web site interface, which includes:
  • a contig assembly browser (click on VIEWER button),
  • BLAST searches (see BLAST button),
  • as well as the sequence files ready for download as compressed tarballs (follow the DATA button).

Proteomic Analyses on Planarian Neoblasts

• Further details are available at the following reference:
      A proteomics approach to decipher the molecular nature of planarian stem cells
      Fernández-Taboada, et al, BMC Genomics, 2011, 12:133.
• Planarian Proteomics page contains both raw and processed data from the proteomics experiments and the posterior computational analyses. This page was provided as additional material on the paper above.

EGASP'05

 
Josep F abril was involved, during his PhD thesis at Roderic Guigó's lab, in the human ENCODE Genome Annotation Assessment Project (EGASP). An analysis workshop was held at the Wellcome Trust Conference Center in Hinxton, UK, on May 6-7, 2005. You can get more information about the event and the results of the evaluations from the following links:

• ENCODE Gene Prediction Workshop.
• Analysis of EGASP'05 workshop predictions.
• The paper published by Guigó et al (Genome Biology, 7-Suppl 1:S2, 2006).

RGASP'09/10

 
We have participated in the evaluation of the submissions by gene prediction groups to the RNA-seq GASP (RGASP). An analysis workshop was held at the Wellcome Trust Conference Center in Hinxton, UK, on November 10-11, 2009. We provide below the related links, including the web page summarizing the whole set of evaluations:

• RGASP Home Page.
• RGASP Summary of Evaluation Results.