Skip to main content
×
Home

A pilot study on transcriptome data analysis of folliculogenesis in pigs

  • G. Tosser-Klopp (a1), K.-A. Lê Cao (a2) (a3), A. Bonnet (a1), N. Gobert (a1), F. Hatey (a1), C. Robert-Granié (a2), S. Déjean (a3), J. Antic (a4), L. Baschet (a4) and M. SanCristobal (a1)...
Abstract

Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from seven RNA follicle pools and several technical replicates were made. The objective of this paper was to state the feasibility of a transcriptomic protocol for the study of folliculogenesis in the pig. A statistical analysis was chosen, relying on the linear mixed model (LMM) paradigm. Low variability within technical replicates was hence checked with a LMM. Relevant genes that might be involved in the studied process were then selected. For the most significant genes, statistical methods such as principal component analysis and unsupervised hierarchical clustering were applied to assess their relevance, and a random forest analysis proved their predictive value. The selection of genes was consistent with previous studies and also allowed the identification of new genes whose role in pig folliculogenesis will be further investigated.

    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      A pilot study on transcriptome data analysis of folliculogenesis in pigs
      Available formats
      ×
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Dropbox account. Find out more about sending content to Dropbox.

      A pilot study on transcriptome data analysis of folliculogenesis in pigs
      Available formats
      ×
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your Google Drive account. Find out more about sending content to Google Drive.

      A pilot study on transcriptome data analysis of folliculogenesis in pigs
      Available formats
      ×
Copyright
Corresponding author
E-mail: gwenola.tosser@toulouse.inra.fr
Footnotes
Hide All
a

These authors have contributed equally to this work.

Footnotes
References
Hide All
Agca C, Ries JE, Kolath SJ, Kim JH, Forrester LJ, Antoniou E, Whitworth KM, Mathialagan N, Springer GK, Prather RS, Lucy MC 2006. Luteinization of porcine preovulatory follicles leads to systematic changes in follicular gene expression. Reproduction 132, 133145.
Algers B, Uvnas-Moberg K 2007. Maternal behavior in pigs. Hormones and Behavior 52, 7885.
Benjamini Y, Hochberg Y 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 57, 289300.
Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR 1999. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Human Molecular Genetics 8, 17151722.
Besnard N, Pisselet C, Monniaux D, Locatelli A, Benne F, Gasser F, Hatey F, Monget P 1996. Expression of messenger ribonucleic acids of insulin-like growth factor binding protein-2, -4, and -5 in the ovine ovary: localization and changes during growth and atresia of antral follicles. Biology of Reproduction 55, 13561367.
Bichard M, David PJ 1985. Effectiveness of genetic selection for prolificacy in pigs. Journal of Reproduction and Fertility. Supplement 33, 127138.
Bonnet A, Frappart PO, Dehais P, Tosser-Klopp G, Hatey F 2006. Identification of differential gene expression in in vitro FSH treated pig granulosa cells using suppression subtractive hybridization. Reproductive Biology and Endocrinology 4, 3510.1186/1477-7827-4-35.
Bonnet A, Iannuccelli E, Hugot K, Benne F, Bonaldo MF, Soares MB, Hatey F, Tosser-Klopp G 2008a. A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9 K micro-array resource generation. BMC Genomics 9, 1710.1186/1471-2164-9-17.
Bonnet A, Le Cao KA, San Cristobal M, Benne F, Robert-Granié C, Law-So G, Fabre S, Besse P, De Billy E, Quesnel H, Hatey F, Tosser-Klopp G 2008b. In vivo gene expression in granulosa cells during pig terminal follicular development. Reproduction 136, 211224.
Breiman L 2001. Random forests. Machine Learning 45, 532.
Buske B, Sternstein I, Brockmann G 2006. QTL and candidate genes for fecundity in sows. Animal Reproduction Science 95, 167183.
Caetano AR, Johnson RK, Ford JJ, Pomp D 2004. Microarray profiling for differential gene expression in ovaries and ovarian follicles of pigs selected for increased ovulation rate. Genetics 168, 15291537.
Churchill GA, Oliver B 2001. Sex, flies and microarrays. Nature Genetics 29, 355356.
Diaz-Uriarte R, Alvarez de Andres S 2006. Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7, 310.1186/1471-2105-7-3.
Duda M 1997. The influence of FSH, LH and testosterone on steroidsecretion by two subpopulations of porcine granulosa cells. Journal of Physiology and Pharmacology 48, 8996.
Eisen MB, Spellman PT, Brown PO, Botstein D 1998. Cluster analysis and display of genome-wide expression patterns. The Proceedings of the National Academy of Sciences of the United States of America 95, 1486314868.
Erickson GF, Magoffin DA, Dyer CA, Hofeditz C 1985. The ovarian androgen producing cells: a review of structure/function relationships. Endocrine Reviews 6, 371399.
Fayad T, Levesque V, Sirois J, Silversides DW, Lussier JG 2004. Gene expression profiling of differentially expressed genes in granulosa cells of bovine dominant follicles using suppression subtractive hybridization. Biology of Reproduction 70, 523533.
Ferré PJ, Liaubet L, Concordet D, Sancristobal M, Uro-Coste E, Tosser-Klopp G, Bonnet A, Toutain PL, Hatey F, Lefebvre HP 2007. Longitudinal analysis of gene expression in porcine skeletal muscle after post-injection local injury. Pharmaceutical Research 24, 14801489.
Foxcroft GR, Hunter MG 1985. Basic physiology of follicular maturation in the pig. Journal of Reproduction and Fertility. Supplement 33, 119.
Foxcroft GR, Hunter MG, Grant SA 1989. The physiology of follicular maturation in the pig. Acta Physiologica Polonica 40, 5363.
Fricke PM, Ford JJ, Reynolds LP, Redmer DA 1996. Growth and cellular proliferation of antral follicles throughout the follicular phase of the estrous cycle in Meishan gilts. Biology of Reproduction 54, 879887.
Garrett WM, Mack SO, Rohan RM, Guthrie HD 2000. In situ analysis of the changes in expression of ovarian inhibin subunit mRNAs during follicle recruitment after ovulation in pigs. Journal of Reproduction and Fertility 118, 235242.
Gasser F, Mulsant P, Gillois M 1985. Long-term multiplication of the Chinese hamster ovary (CHO) cell line in a serum-free medium. In Vitro Cellular and Developmental Biology 21, 588592.
Guthrie HD, Barber JA, Leighton JK, Hammond JM 1994. Steroidogenic cytochrome P450 enzyme messenger ribonucleic acids and follicular fluid steroids in individual follicles during preovulatory maturation in the pig. Biology of Reproduction 51, 465471.
Hirshfield AN 1986. Patterns of [3H] thymidine incorporation differ in immature rats and mature, cycling rats. Biology of Reproduction 34, 229235.
Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genetics 29, 389395.
Kao LC, Germeyer A, Tulac S, Lobo S, Yang JP, Taylor RN, Osteen K, Lessey BA, Giudice LC 2003. Expression profiling of endometrium from women with endometriosis reveals candidate genes for disease-based implantation failure and infertility. Endocrinology 144, 28702881.
Kerr MK, Churchill GA 2001. Experimental design for gene expression microarrays. Biostatistics 2, 183201.
Knox RV 2005. Recruitment and selection of ovarian follicles for determination of ovulation rate in the pig. Domestic Animal Endocrinology 29, 385397.
Le Cao KA, Goncalves O, Besse P, Gadat S 2007. Selection of biologically relevant genes with a wrapper stochastic algorithm. Statistical Applications in Genetics and Molecular Biology 6, Article 29.
Liaw A, Wiener M 2002. Classification and regression by random Forest. The Newspaper of R Project 2, 1822.
Lopez F, Rougemont J, Loriod B, Bourgeois A, Loi L, Bertucci F, Hingamp P, Houlgatte R, Granjeaud S 2004. Feature extraction and signal processing for nylon DNA microarrays. BMC Genomics 5, 38.
May JV, Schomberg DW 1984. Developmental coordination of luteinizing hormone/human chorionic gonadotropin (hCG) receptors and acute hCG responsiveness in cultured and freshly harvested porcine granulosa cells. Endocrinology 114, 153163.
Monniaux D 1987. Short-term effects of FSH in vitro on granulosa cells of individual sheep follicles. Journal of Reproduction and Fertility 79, 505515.
Muller C, Denis M, Gentzbittel L, Faraut T 2004. The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. Nucleic Acids Research 32, W429W434.
Patterson HD, Thompson R 1971. Recovery of inter-block information when block sizes are unequal. Biometrika 58, 545554.
Pisselet C, Clement F, Monniaux D 2000. Fraction of proliferating cells in granulosa during terminal follicular development in high and low prolific sheep breeds. Reproduction, Nutrition, Development 40, 295304.
Raychaudhuri S, Stuart JM, Altman RB 2000. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pacific Symposium on Biocomputing 5, 452463.
Seber G 1984. Multivariate observations. Wiley, New York, NY.
Statistical Analysis Systems Institute 1999. SAS/STAT Software, version 8. SAS Institute Inc., Cary, NC.
Tosser-Klopp G, Benne F, Bonnet A, Mulsant P, Gasser F, Hatey F 1997. A first catalog of genes involved in pig ovarian follicular differentiation. Mammalian Genome 8, 250254.
van der Lende T, Knol EF, Leenhouwers JI 2001. Prenatal development as a predisposing factor for perinatal losses in pigs. Reproduction 58(suppl.), 247261.
Varani S, Elvin JA, Yan C, DeMayo J, DeMayo FJ, Horton HF, Byrne MC, Matzuk MM 2002. Knockout of pentraxin 3, a downstream target of growth differentiation factor-9, causes female subfertility. Molecular Endocrinology 16, 11541167.
Vizirianakis IS, Pappas IS, Gougoumas D, Tsiftsoglou AS 1999. Expression of ribosomal protein S5 cloned gene during differentiation and apoptosis in murine erythroleukemia (MEL) cells. Oncology Research 11, 409419.
Whitworth KM, Agca C, Kim JG, Patel RV, Springer GK, Bivens N, Forrester LJ, Mathialagan N, Green JA, Prather RS 2005. Transcriptional profiling of pig embryogenesis by using a 15k member unigene set specific for pig reproductive tissues and embryos. Biology of Reproduction 72, 14371451.
Wu H, Kerr MK, Cui X, Churchill GA 2003. MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In The analysis of gene expression data: methods and software (ed. G Parmigiani, ES Garrett, RA Irizarry and SL Zeger). Springer, New York, NY.
Yeung KY, Ruzzo WL 2001. Principal component analysis for clustering gene expression data. Bioinformatics 17, 763774.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

animal
  • ISSN: 1751-7311
  • EISSN: 1751-732X
  • URL: /core/journals/animal
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords:

Metrics

Full text views

Total number of HTML views: 6
Total number of PDF views: 54 *
Loading metrics...

Abstract views

Total abstract views: 106 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 21st November 2017. This data will be updated every 24 hours.