Open Access Research

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays

Adnane Sellam12*, Hervé Hogues1, Christopher Askew13, Faiza Tebbji13, Marco van het Hoog1, Hugo Lavoie4, Carol A Kumamoto5, Malcolm Whiteway13 and André Nantel12*

Author Affiliations

1 Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montréal, Québec, H4P 2R2, Canada

2 Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Québec, H3A 1B1, Canada

3 Department of Biology, McGill University, 1205 Docteur Penfield, Montréal, Québec, H3A 1B1, Canada

4 Intracellular Signaling Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, 2900 boulevard Édouard-Montpetit, Montreal, Quebec, H3C 3J7, Canada

5 Department of Molecular Biology and Microbiology, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA

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Genome Biology 2010, 11:R71  doi:10.1186/gb-2010-11-7-r71

Published: 9 July 2010

Additional files

Additional file 1:

Figure S1. GO analysis of the 28% of nuclear genes not expressed in this study.

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Additional file 2:

Table S1. Genome-scale detection of unannotated transcribed segments in C. albicans growing in different conditions.

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Additional file 3:

Table S15. List of nested or overlapping genes validated in this work.

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Additional file 4:

Table S2. List of detected ORFs and pseudogenes.

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Additional file 5:

Table S3. List of ORFs exhibiting long 5' and 3' UTRs (>240 bp)

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Additional file 6:

Table S4. Gene Ontology analysis of ORFs with long 5' and 3' UTR regions (>330 bp).

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Additional file 7:

Tables S5, S6, and S7. Genome-wide detection of ncRNAs: Table S5, AS transcripts; Table S6, housekeeping ncRNAs; and Table S7, RT-qPCR validation of randomly selected ncRNAs.

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Additional file 8:

Figure S2. Transcription and RNAP I and III occupancies within the rDNA locus.

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Additional file 9:

Tables S8 and S9. Detection of RNAP III binding peaks (Table S8) and genomic organization and coordinates of telomeric ncRNA (TelRs; Table S9).

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Additional file 10:

Figure S3. Transcription and RNAP III occupancy of ncRNAs. tRNAs (a, b), RPR1 (b) and an unknown ncRNA (c) are represented.

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Additional file 11:

Table S10. GO process annotation of differentially regulated annotated features using the CGD GO Term Finder [27].

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Additional file 12:

Table S11. List of differentially expressed ORFs in hyphae, biofilm and caecum-grown cells.

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Additional file 13:

Figure S4. Real-time quantitative PCR validation of candidate genes differentially expressed in caecum-grown Candida cells. Both heme-binding (a) and carbohydrate catabolism genes (b) were considered.

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Additional file 14:

Table S12. Genome-scale detection of differentially expressed unannotated transfrags in C. albicans.

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Additional file 15:

Table S13. C. albicans strains used in the study [87,88].

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Additional file 16:

Table S14. Primers used in this study.

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