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- Creator:
- Delarosa, Beverly
- Description:
- An Analysis for 24 Cancers in 30 Countries in 2012: Incidence Rates and Treatment Effectiveness
Beverly Delarosa
Statistics
2016-05
- Resource Type:
- Project
- Campus Tesim:
- Long Beach
- Creator:
- Weerackoon, Ranil
- Description:
- Formulating Optimal Betting Strategies Through a Statistical Prediction of the Outcome and Margin of Victory of NFL Games
Ranil Weerackoon
Statistics
2015-05
- Resource Type:
- Project
- Campus Tesim:
- Long Beach
- Creator:
- Schiller, Kyle
- Description:
- The intent of this study is to further the understanding of polyphenol oxidase's (PPO) functional characteristics in walnut and the plant kingdom through the use of RNA-seq de novo assembly and differential expression analysis. We begin the study with three wild-type (natural unchanged PPO activity) and three PPO-silenced ( > 95% reduction in PPO activity) samples from the walnut species Juglans regia, containing a total of approximately 106 million and 122 million paired-end reads, respectively. Since no reference genome exists, we utilized Trinity, an RNA-seq de novo transcriptome assembler, in order to reconstruct full-length transcripts and alternatively spliced isoforms from our RNA-seq data. A total of 110,068 transcripts were assembled with a N50 contig length of 1,776. We then aligned our RNA-seq data to the assembled transcriptome using Bowtie to assess the quality of the assembly. Approximately 92% of the aligned RNA-seq reads were proper pairs (i.e., each end of a paired-end read successfully mapped to the same contig). Next, we used RNA-seq by Expectation-Maximization (RSEM), which is a software tool that estimates gene and isoform expression levels from our paired-end RNA-seq data. The expression estimates generated by RSEM from both our assembled transcriptome and a reference transcriptome were used with two differential expression analysis tools, edgeR and DESeq, in order to determine which genes are being differentially expressed in PPO-silenced plants as compared to wild-type. Using edgeR and a false discovery rate of 0.001, we found 91 genes from our assembled transcriptome and 130 genes from the reference transcriptome to be differentially expressed. Using DESeq, we discovered 69 genes from our assembled transcriptome and 46 genes from the reference transcriptome to be differentially expressed based on an adjusted p-value of 0.05 or lower. We then employed BLAST (BLASTn), which compares a nucleotide query sequence against a nucleotide sequence database, to conduct various comparisons between our Trinity assembly, the reference assembly, and our differentially expressed sets discovered using edgeR and DESeq. One of the results determined that 8 of the 91 differentially expressed genes found using edgeR, and 7 of the 69 differentially expressed genes found using DESeq were absent from the reference transcriptome.
- Resource Type:
- Project
- Campus Tesim:
- San Marcos
- Department:
- Computer Science