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 mapping, transcript and isoform detection,and differential expression were done using the Illumina Pipeline
  
• 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.
  
• TF Enrichment
  TF 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
  

Venn Diagrams

Circadian Transcripts

Phase Analysis

Period

Heatmaps

Circadian in BOTH Conditions

Amplitude

Data Download

• Raw FPKM Table for Condition 1: Table
• Raw FPKM Table for Condition 2: Table
• Circadian Genes in Condition 1: Table
• Circadian Genes in Condition 2: Table
• (BOTH) Circadian Genes in Both Conditions: Table

Data Visualization

Pathway Enrichment

• Pathway Enrichment in Condition1: Pathway Analysis
  
• Pathway Enrichment in Condtion2: Pathway Analysis
  
• Pathway Enrichment (BOTH): Pathway Analysis

Data Download

Pathway Enrichment

• Pathway Enrichment EXCEL: Excel Table
  
• Pathway Enrichment EXCEL: Excel Table
  
• Pathway Enrichment (BOTH) EXCEL: Excel Table

MotifMap TFBS, CHiPSeq, and RBP Enrichment

• Factor Enrichment in Condition1
• Factor Enrichment in Condition2
• Factor Enrichment in Both

Data Download

• TFBS Condition1 Excel
• TFBS Condition2 Excel
• TFBS (Both) Excel

Data Download

• List of circadian targets: list
  
• List of circadian TFs: list
  
• List of circadian RBPs: list

Data Visualization