Literature DB >> 33625717

How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b.

Yorick Bernardus Cornelis van de Grift1, Nika Heijmans1, Renée van Amerongen2.   

Abstract

An increasing number of '-omics' datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific '-omics' datasets and thereby expand the in silico toolbox.

Entities:  

Keywords:  Beta-catenin; CTNNB1; Gene regulation; In silico analysis; Wnt signaling; Wnt7b

Mesh:

Substances:

Year:  2021        PMID: 33625717      PMCID: PMC7960620          DOI: 10.1007/s10911-020-09474-z

Source DB:  PubMed          Journal:  J Mammary Gland Biol Neoplasia        ISSN: 1083-3021            Impact factor:   2.673


  80 in total

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Journal:  Cancer Cell       Date:  2011-07-12       Impact factor: 31.743

2.  Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Authors:  Hannah A Pliner; Jonathan S Packer; José L McFaline-Figueroa; Darren A Cusanovich; Riza M Daza; Delasa Aghamirzaie; Sanjay Srivatsan; Xiaojie Qiu; Dana Jackson; Anna Minkina; Andrew C Adey; Frank J Steemers; Jay Shendure; Cole Trapnell
Journal:  Mol Cell       Date:  2018-08-02       Impact factor: 17.970

Review 3.  Exploiting human--fish genome comparisons for deciphering gene regulation.

Authors:  Nadav Ahituv; Edward M Rubin; Marcelo A Nobrega
Journal:  Hum Mol Genet       Date:  2004-10-01       Impact factor: 6.150

4.  Up-regulation of Wnt7b rather than Wnt1, Wnt7a, and Wnt9a indicates poor prognosis in breast cancer.

Authors:  Jian Chen; Tian-Yu Liu; Hai-Tao Peng; Yan-Qing Wu; Li-Li Zhang; Xiao-Hong Lin; Yuan-Hui Lai
Journal:  Int J Clin Exp Pathol       Date:  2018-09-01

5.  Multiple knockout mouse models reveal lincRNAs are required for life and brain development.

Authors:  Martin Sauvageau; Loyal A Goff; Simona Lodato; Boyan Bonev; Abigail F Groff; Chiara Gerhardinger; Diana B Sanchez-Gomez; Ezgi Hacisuleyman; Eric Li; Matthew Spence; Stephen C Liapis; William Mallard; Michael Morse; Mavis R Swerdel; Michael F D'Ecclessis; Jennifer C Moore; Venus Lai; Guochun Gong; George D Yancopoulos; David Frendewey; Manolis Kellis; Ronald P Hart; David M Valenzuela; Paola Arlotta; John L Rinn
Journal:  Elife       Date:  2013-12-31       Impact factor: 8.140

6.  R-spondin1 is a novel hormone mediator for mammary stem cell self-renewal.

Authors:  Cheguo Cai; Qing Cissy Yu; Weimin Jiang; Wei Liu; Wenqian Song; Hua Yu; Lei Zhang; Ying Yang; Yi Arial Zeng
Journal:  Genes Dev       Date:  2014-09-26       Impact factor: 11.361

7.  Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

Authors:  Shenglin Mei; Qian Qin; Qiu Wu; Hanfei Sun; Rongbin Zheng; Chongzhi Zang; Muyuan Zhu; Jiaxin Wu; Xiaohui Shi; Len Taing; Tao Liu; Myles Brown; Clifford A Meyer; X Shirley Liu
Journal:  Nucleic Acids Res       Date:  2016-10-26       Impact factor: 16.971

8.  A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis.

Authors:  Paul Krimpenfort; Margriet Snoek; Jan-Paul Lambooij; Ji-Ying Song; Robin van der Weide; Rajith Bhaskaran; Hans Teunissen; David J Adams; Elzo de Wit; Anton Berns
Journal:  Nat Commun       Date:  2019-03-29       Impact factor: 14.919

9.  Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development.

Authors:  Rajshekhar R Giraddi; Chi-Yeh Chung; Richard E Heinz; Ozlen Balcioglu; Mark Novotny; Christy L Trejo; Christopher Dravis; Berhane M Hagos; Elnaz Mirzaei Mehrabad; Luo Wei Rodewald; Jae Y Hwang; Cheng Fan; Roger Lasken; Katherine E Varley; Charles M Perou; Geoffrey M Wahl; Benjamin T Spike
Journal:  Cell Rep       Date:  2018-08-07       Impact factor: 9.423

10.  SpatialDB: a database for spatially resolved transcriptomes.

Authors:  Zhen Fan; Runsheng Chen; Xiaowei Chen
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

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  2 in total

1.  Integrated Analysis of Transcriptome mRNA and miRNA Profiles Reveals Self-Protective Mechanism of Bovine MECs Induced by LPS.

Authors:  Ling Chen; Xiaolin Liu; Zhixiong Li; Jian Wang; Rongfu Tian; Huilin Zhang
Journal:  Front Vet Sci       Date:  2022-06-23

2.  Unraveling the Breast: Advances in Mammary Biology and Cancer Methods.

Authors:  Teresa Monkkonen; Gunnhildur Ásta Traustadóttir; Zuzana Koledova
Journal:  J Mammary Gland Biol Neoplasia       Date:  2021-01-21       Impact factor: 2.698

  2 in total

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