Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Research

Regulation of alternative splicing by the circadian clock and food related cues

Nicholas J McGlincy1*, Amandine Valomon12, Johanna E Chesham1, Elizabeth S Maywood1, Michael H Hastings1* and Jernej Ule1*

Author Affiliations

1 MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK

2 Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Z├╝rich, Switzerland

For all author emails, please log on.

Genome Biology 2012, 13:R54  doi:10.1186/gb-2012-13-6-r54

Published: 21 June 2012

Additional files

Additional file 1:

Supplemental Data. Supplemental Figures 1 to 10 and associated legends, supplemental experimental procedures and supplemental references.

Format: PDF Size: 7.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Table S1. Information regarding the positive probesets identified by the FIRMA analysis, compiled using the exonmap and xmapcore bioconductor packages [1-3]. probeset refers to the exon-probeset of interest. Fields: sotaCluster refers to the self-organizing tree algorithm (sota) cluster the probeset is part of (Figure 1b); adj.P.Val.Limma refers to the multiple-testing corrected P-value associated with the one-way ANOVA for an effect of time executed in limma [68,81] (see Materials and methods); ensExonID refers to the Ensembl [82] identifier for the exon within which the probeset is located; probeLoc refers to the mm9 genomic co-ordinates for the probeset of interest; exonSequence refers to the sequence of the exon identified by ensExonID; divisableBy3 indicates whether the exon's length is a multiple of three or not; ensGeneID refers to the Ensembl [82] identifier for the gene within which the exon identified by ensExonID is located; geneLoc refers to the mm9 genomic co-ordinates for the gene of interest; validation refers to validation status of the exon of interest (nd, not determined); description refers to official long name of the gene of interest.

Format: XLS Size: 63KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Table S2. Summary of the functional annotation data obtained for the positive genes from the FIRMA analysis, using DAVID [76]. Fields: Category refers to the source of the functional annotation term; Term refers to the particular enriched annotation term; PValue refers to the raw P-value associated with the enrichment of the term; Genes refers to the gene symbols of those genes from the list that contribute to the enrichment of this term; Fold Enrichment refers to the level of enrichment of this term over the background distribution; Benjamini refers to the P-value for enrichment after correction for multiple testing according to the method of Benjamini and Hochberg [83]; ofInterest refers to whether this term was considered pertinent to our analysis.

Format: XLS Size: 36KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Table S3. Results of the Gene Ontology term [29] enrichment analysis performed using WebGestalt [77].

Format: XLS Size: 66KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Table S4. Results of the KEGG pathway [28,84,85] enrichment analysis performed using WebGestalt [77].

Format: XLS Size: 22KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Table S5. Output of MotifScanner from the analysis of predicted clock transcription factor binding sites in the proximal promoter region of circadian splicing factors/RBPs. refseq refers to the Refseq mRNA relative to which the examined sequence was extracted. location refers to the genomic co-ordinates of the sequence examined.

Format: XLS Size: 46KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Table S6. Correlations between microarray data from Hughes et al. [41] and QPCR measurements from this study for circadian splicing factors/RBPs identified from Hughes et al. [41]. Quality refers to a manual assessment of the robustness of the circadian expression profile for that probeset, 1 being best and 3 being worst.

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Table S7. Details of all the oligonucleotides used in this study.

Format: XLS Size: 42KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data