Runan Yao
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View article: RNA sequencing and iTRAQ proteomic data from an experiment examining the influence of conceptus presence and preovulatory estradiol on endometrial gene transcripts and proteins around maternal recognition of pregnancy in beef cattle
RNA sequencing and iTRAQ proteomic data from an experiment examining the influence of conceptus presence and preovulatory estradiol on endometrial gene transcripts and proteins around maternal recognition of pregnancy in beef cattle Open
RNA sequencing reads and isobaric tags for a relative and absolute quantification (iTRAQ)-Based Proteomic Data were used to determine the impact of conceptus presence and preovulatory estradiol concentration on function of the d16 uterus i…
View article: Influence of estradiol on bovine trophectoderm and uterine gene transcripts around maternal recognition of pregnancy
Influence of estradiol on bovine trophectoderm and uterine gene transcripts around maternal recognition of pregnancy Open
Embryo survival and pregnancy success is increased among animals that exhibit estrus prior to fixed time-artificial insemination, but there are no differences in conceptus survival to d16. The objective of this study was to determine effec…
View article: ShinyGO: a graphical gene-set enrichment tool for animals and plants
ShinyGO: a graphical gene-set enrichment tool for animals and plants Open
Motivation Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as gene ontology (GO) and other databases. Results To c…
View article: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
View article: Additional file 5: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 5: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
An example of customized R code generated by iDEP. This code is generated for the analysis of the Hoxa1 dataset. (R 11 kb)
View article: Additional file 4: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 4: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
DNA microarray data of thymic tissue of down syndrome infants. Data is from GSE69210 from NCBI. (CSV 4745 kb)
View article: Additional file 7: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 7: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Core R functions in iDEP. This code is generated for the analysis of the Hoxa1 dataset. (R 172 kb)
View article: Additional file 6: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 6: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
An example of R Markdown file generated by iDEP. This code is generated for the analysis of the Hoxa1 dataset. (RMD 15 kb)
View article: Additional file 8: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 8: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Read count file for the mouse ionization/p53 dataset. This file was used in our analysis. (CSV 1513 kb)
View article: Additional file 9: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 9: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Experiment design file for the mouse ionization/p53 dataset. This file was used in our analysis. (CSV 226 bytes)
View article: Additional file 1: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 1: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Tables S1-S16. Table S1. contains list of 220 species covered by current version of iDEP. Table S2. include the 2196 types of gene IDs that can be recognized. Tables S3-S16. are results from the analyses of two example datasets. (XLSX 1970…
View article: Additional file 2: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Additional file 2: of iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Read count file for Hoxd1 knockdown example. This file is derived from short read archive (SRA) SRP012607 using Sailfish. (CSV 718 kb)
View article: Game Theoretical Approach for Joint Relay Selection and Resource Allocation in Mobile Device Networks
Game Theoretical Approach for Joint Relay Selection and Resource Allocation in Mobile Device Networks Open
With the improvement of hardware, more and more multimedia applications are allowed to run in the mobile device. However, due to the limited radio bandwidth, wireless network performance becomes a critical issue. Common mobile solutions ar…