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Ethanol Project - Analysis Results
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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 Diet
  • List of Conditions
  • List of Groups
  • List of Time Points
  • List of Technical Groups
  • List of Replicates

Analysis Procedure

  • Differental Analysis Analysis of disrupted timepoints was done via CyberT
  • 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.
    Login:
    User: baldi
    Password: circadian
    Select Transcriptome
    Datasets: Ethanol Liver Acute (Biocycle)
    Ethanol Liver Chronic (Biocycle)
    Ethanol Liver Acute (JTK)
    Ethanol Liver Acute (JTK)
    Search by Gene Symbol (provided in analysis)

CyberT Results

See NFKB1 Analysis Report for Detailed Results

Venn Diagrams

Circadian Transcripts


Circadian Transcription Factors


Phase Radar Plots

Circadian in Alone

Circadian in Both


Amplitude Histograms

Alone (Selected Condition)

Both (Selected Condition)

Period Histograms

Alone (Selected Condition)

Both (Selected Condition)

Comparison Plots

Heatmaps

Alone (Selected Condition)

Both (Selected Condition)


Data Download

Data Visualization

Pathway Enrichment

Acetyl CoA Related Pathways

NAD+ Pathways

Ethanol Pathways

Xenobiotics Pathways

Data Download

Pathway Enrichment

DAVID Analysis

MotifMap TFBS, CHiPSeq, and RBP Enrichment

Data Download

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