This section provides the identifiers and notations used to report the analysis results
on this website.
It also provides a description of some parts of the analysis and
some comments that may help understand the results.
Analysis Procedure
- RNA Seq Analysis
Read trimming was done using Trimmomatic. The first 5 base pairs on both reads were cropped.
Read mapping, transcript and isoform detection,and differential expression were done using the Tuxedo Suite (Tophat and Cufflinks)
Tuxedo
- Detecting Oscillation
Detecting oscillating transcripts (P-Value, Q-Value, Period, Amplitude, Lag) was done via:
BioCycle
- Functional Analysis
Functional Analysis was performed using GO Terms
Please click on links under tab for detailed reports of GO Terms for oscillating transcripts.
- TFBS Enrichment
TFBS Enrichment was performed using MotifMap and CHiPSeq experiments obtained from ENCODE
Please use table to see specific experiment identifiers.
- Visualization
Please visit Circadiomics for transcript visualization.
Select Transcriptome
Datasets:
MOUSE_SCN_SALINE (Biocycle)
MOUSE_SCN_DZnep (Biocycle)
Worg