title: Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq.
abstract: BACKGROUND
  Molecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue.
  
  
  RESULTS
  As a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR.
  
  
  CONCLUSIONS
  Results of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues.
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea, 151-741, Republic of Korea. nijorral@gmail.com.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea. nijorral@gmail.com.
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA. caetano1@illinois.edu.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anolles
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA. rodrgzzs@illinois.edu.
authors.forename: Sandra
authors.initials: S
authors.lastname: Rodriguez-Zas
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. skasnu@snu.ac.kr.
authors.forename: Sojeong
authors.initials: S
authors.lastname: Ka
authors.affiliation: Division of Animal Products R&D, National Institute of Animal science, #1500 Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 565-851, Republic of Korea. jeongjinyoung73@gmail.com.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Jeong
authors.affiliation: Department of food science and technology, Sejong University, 98 Gun-Ja-Dong, Seoul, 143-747, Republic of Korea. sungkwonpark@hotmail.com.
authors.forename: Sungkwon
authors.initials: S
authors.lastname: Park
authors.affiliation: Department of food science and technology, Sejong University, 98 Gun-Ja-Dong, Seoul, 143-747, Republic of Korea. mjkim00@korea.kr.
authors.forename: Min Ji
authors.initials: MJ
authors.lastname: Kim
authors.affiliation: Department of Swine & Poultry Science, National College of Agriculture and Fisheries, #1515 Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 560-500, Republic of Korea. nhowgook@korea.kr.
authors.forename: Whan-Gook
authors.initials: WG
authors.lastname: Nho
authors.affiliation: CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea. seoae@cnkgenomics.com.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea, 151-741, Republic of Korea. heebal@snu.ac.kr.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.|Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. heebal@snu.ac.kr.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea, 151-741, Republic of Korea. hyunj68@korea.kr.|Division of Animal Products R&D, National Institute of Animal science, #1500 Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 565-851, Republic of Korea. hyunj68@korea.kr.
authors.forename: Hyun-Jeong
authors.initials: HJ
authors.lastname: Lee
mesh_terms: D000818:Animals; D002417:Cattle; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics*; D051381:Rats; D012727:Sex Characteristics
chemical_list: D012313:RNA
references.citation: BMC Bioinformatics. 2013 Feb 27;14:70
references.pmid: 23444967
references.citation: Hum Mol Genet. 2002 Jun 1;11(12):1409-19
references.pmid: 12023983
references.citation: Genet Sel Evol. 2009 Jun 25;41:36
references.pmid: 19555501
references.citation: BMC Genomics. 2015 Nov 09;16:914
references.pmid: 26552448
references.citation: Genome Res. 2006 Aug;16(8):995-1004
references.pmid: 16825664
references.citation: Nat Rev Neurosci. 2003 Aug;4(8):649-61
references.pmid: 12894240
references.citation: J Lipid Res. 2006 Dec;47(12):2690-700
references.pmid: 17003504
references.citation: Mol Cell Biol. 2012 Nov;32(22):4611-27
references.pmid: 22966202
references.citation: Bioinformatics. 2010 Jan 1;26(1):139-40
references.pmid: 19910308
references.citation: BMC Genomics. 2013 May 25;14:350
references.pmid: 23705625
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21878-83
references.pmid: 21098290
references.citation: J Anim Sci. 2002 Jan;80(1):129-36
references.pmid: 11831510
references.citation: Life Sci. 2007 Feb 13;80(10):940-4
references.pmid: 17174342
references.citation: Curr Opin Clin Nutr Metab Care. 2001 Nov;4(6):499-502
references.pmid: 11706283
references.citation: Nucleic Acids Res. 2012 May;40(10):4288-97
references.pmid: 22287627
references.citation: Nat Protoc. 2009;4(1):44-57
references.pmid: 19131956
references.citation: Nutrition. 2004 Jan;20(1):115-20
references.pmid: 14698025
references.citation: J Biomed Sci. 2006 Nov;13(6):845-51
references.pmid: 16944268
references.citation: Neuropsychopharmacology. 2004 Feb;29(2):373-84
references.pmid: 14583743
references.citation: Bioinformatics. 2014 Aug 1;30(15):2114-20
references.pmid: 24695404
references.citation: Genome Biol. 2014;15(12):550
references.pmid: 25516281
references.citation: Mol Biol Rep. 2012 May;39(5):6113-21
references.pmid: 22223295
references.citation: Eur J Neurosci. 2005 Jun;21(11):3017-22
references.pmid: 15978012
references.citation: BMC Bioinformatics. 2005 May 29;6:129
references.pmid: 15921534
references.citation: Genet Res. 2001 Apr;77(2):123-8
references.pmid: 11355567
references.citation: Horm Behav. 1994 Dec;28(4):464-76
references.pmid: 7729815
references.citation: Asian-Australas J Anim Sci. 2015 Jul;28(7):911-21
references.pmid: 26104394
references.citation: BMC Genomics. 2015 Apr 01;16:256
references.pmid: 25887412
references.citation: Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15224-8
references.pmid: 14638941
references.citation: Horm Metab Res. 2002 May;34(5):223-8
references.pmid: 12063633
references.citation: BMC Genomics. 2011 Jan 07;12:13
references.pmid: 21214936
references.citation: Mol Endocrinol. 2006 Nov;20(11):2613-29
references.pmid: 16543404
references.citation: J Anim Sci. 1998 Sep;76(9):2272-8
references.pmid: 9781482
references.citation: Brain Res Brain Res Rev. 1999 Aug;30(2):135-52
references.pmid: 10525171
references.citation: Mol Endocrinol. 2008 Aug;22(8):1962-74
references.pmid: 18483176
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Genomics. 2005 Jun;85(6):679-87
references.pmid: 15885495
references.citation: Nat Methods. 2012 Mar 04;9(4):357-9
references.pmid: 22388286
references.citation: J Bacteriol. 2003 Apr;185(7):2080-95
references.pmid: 12644477
references.citation: J Data Sci. 2006;4(3):323-341
references.pmid: 20016750
references.citation: BMC Bioinformatics. 2010 Aug 03;11:408
references.pmid: 20678237
references.citation: Bioinformatics. 2022 May 13;38(10):2943-2945
references.pmid: 35561197
references.citation: Endocrinology. 1978 Jul;103(1):141-51
references.pmid: 744065
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12909-14
references.pmid: 18753621
references.citation: Bioinformatics. 2002 Apr;18(4):546-54
references.pmid: 12016052
references.citation: Genome Biol. 2013 Apr 25;14(4):R36
references.pmid: 23618408
references.citation: J Proteome Res. 2013 Mar 1;12(3):1199-210
references.pmid: 23379789
references.citation: J Osteoporos. 2011;2011:702735
references.pmid: 22007336
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Biostatistics. 2009 Jul;10(3):468-80
references.pmid: 19329818
references.citation: Endocrine. 2001 Jul;15(2):225-30
references.pmid: 11720251
references.citation: Trends Endocrinol Metab. 2004 Jan-Feb;15(1):6-11
references.pmid: 14693420
references.citation: Brain Res. 2004 Jul 2;1013(1):107-16
references.pmid: 15196973