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.

Experimental Design

• List of Conditions
• List of Groups
• List of Time Points
• List of Technical Groups
• List of Replicates

Analysis Procedure

• Detecting Oscillation
  Detecting oscillating transcripts (P-Value, Q-Value, Period, Amplitude, Lag) was done via 2 Methods:
  BioCycle
  JTK
  
• Functional Analysis
  Functional Analysis was performed using DAVID and GO Terms
  Please click on links under tab for detailed reports of DAVID clustering/enrichment and 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.
  User: baldi
  Password: circadian
  Select Transcriptome
  Datasets:
  AHCY WT (Biocycle)
  AHCY KO (Biocycle)
  

Venn Diagrams

Circadian Transcripts

Amplitude Histogram

Circadian in WT-Alone

Circadian in KO-Alone

Circadian in BOTH (WT) Conditions

Circadian in BOTH (KO) Conditions

Period Histogram

Circadian in WT-Alone

Circadian in KO-Alone

Circadian in BOTH (WT) Conditions

Circadian in BOTH (KO) Conditions

Phase Histogram

Circadian in WT-Alone

Circadian in KO-Alone

Circadian in BOTH (WT) Conditions

Circadian in BOTH (KO) Conditions

Phase Radar

Circadian in WT & KO Alone

Circadian in WT & KO Both

Heatmaps

Circadian in WT-Alone

Circadian in KO-Alone

Circadian in BOTH (WT) Conditions

Circadian in BOTH (KO) Conditions

Heatmaps (Core Circadian TFs)

Circadian Core Clock in WT

Circadian Core Clock in KO

Data Download

• Dataset: Table
• Genes: Table
• TFs: Table
• (BOTH) Genes: Table
• (BOTH) TFs: Table
  

Data Visualization

Pathway Enrichment

• Pathway Enrichment: Pathway Analysis
  
• Pathway Enrichment (BOTH): Pathway Analysis

Data Download

Pathway Enrichment

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

DAVID Analysis

• DAVID Cluster Report: Clustering Table
  
• DAVID Cluster Report (BOTH): Clustering Table

MotifMap TFBS, CHiPSeq, and RBP Enrichment

• Enriched Report
• Enriched Report Both

Data Download

• TFBS Excel
• TFBS (Both) Excel

Motifmap Architecture

Top 20 TFs by Coverage (Selected Condition)

Please click a row to easily view all the information. Selecting Column Visibility can remove GO Terms or GeneLists for an easier read out of the ranked TFs. You can search for key words in GO terms column. Rows are sortable by clicking on columns.

In-Phase is the percent of oscillating genes that are targets of an oscillating TF in the selected condition and in-phase +/- 2 hours

Oscillating TF is the percent of oscillating genes that are targets of an oscillating TF in the selected condition.

Any TF is the percent of oscillating genes that are targets of any TF regardless of its oscillation in the selected condition.

Ranked GO Terms are the list of GO terms associated with oscillating targets ordered by occurence. This is more of a guide for further examination. Some post filters were put in place.

Targets is the list of oscillating targets.

Data Visualization