Help

Topics

Selecting Datasets

Select any dataset from the Transcriptome, Metabolome, Proteome or Acetylome dropdowns. Datasets are added to the dropdown menu title "Selected Datasets" as shown below. Clicking the yellow dataset name will display information about the dataset including the citation, species, omic type, and any others datasets included in the study in a pop-up window. Remove a dataset by selecting the red "X" button. All queries will be run against all the datasets that are currently selected

Yellow Button For Dataset Details and Red Button to Remove Dataset

Example of Dataset Details Pop-Up

Dataset Details

Further details for each dataset are included on the Dataset page. This can be accessed from any location by clicking on the "Datasets" button in the navigation bar on the upper left of the page. There are four separate tabs for each omic type. Details include a brief description, species, specific tissue, a broader tissue classification, experimental condition, GEO accession, experiment type, information on animal subject, experimental protocol, a link to the original publication, and number of replicates and timepoints. Keyword search can be performed on any category for available information.

Location of Data Page Link and Keyword Search

Querying Species

Begin typing the name of a species for the omic type in the main search bar as shown below. Autocomplete will give suggestions for species symbols that are currently available in all the selected datasets.

Clicking "Display" will show trends for the current query in the currently selected datasets. Clicking "Clear" will clear the main display and statistics table and remove all previous queries.

Display and Clear Options

Performing Batch Queries

Dataset Batch

Adding multiple datasets to the "Selected Datasets" dropdown allows the user to perform a query for a given species on several datasets at once. Any combination of datasets can be added to the current "Selected Datasets" list. See Selecting Datasets for more information on using the dropdown menus.

Selection of Two Datasets

Symbol Batch

To query multiple species against the currently selected datasets at once, separate each species symbol by a semi-colon as shown below.

Batch Species Query

Displaying Results

Removing Queries

Selecting the "Remove" option for a particular species / dataset trend will remove this result from the main display and the statistics table. The button is show below.

Normalization

Toggling the "Normalization" between Off and On will update the main display between expression results provided in the public available datasets and the same values normalized between 0 and 1. An example is shown below. This feature is useful when experiments have diverse reported expression values.

Software

Toggling the "Software" tab between "BIO_CYCLE" and "JTK_CYCLE" will update the current display table with statistics produced from the respective software packages. For more information on these statistics, see Statistics.

Normalization and Software Toggles

Filtering Datasets

The user can filter datasets by species, broad tissue classification (Liver, Muscle, Brain, etc.), and dataset experimental type (Control, Knock-Out, Knock-Down, Drug Treatment, etc.). Selecting the "Clear Filters" option at the very top of the filter menu shown below removes all of the currently applied filters.

Statistics

P-Value

Adjusted p-value as reported from BIO_CYCLE or JTK_CYCLE. Generally, a p-value < 0.05 is considered statistically significant.

P-Value

Benjamini-Hochbeg FDR as reported from BIO_CYCLE or JTK_CYCLE.

Amplitude

Amplitude of periodic signal from peak to trough.

Lag

Phase shift of periodic signal from sine function.

Period

Both BIO_CYCLE and JTK_CYCLE have been set to search for statistically significant signals with periods between 20 and 28 hours.

Data Table Display

Downloadable Content

The current display image can be downloaded in PNG or SVG format by clicking the buttons within the query search bar as shown below.

The current table of statistics results can be downloaded in an excel compatible format by clicking the "Excel" button on the upper right side of the statistics table as shown below. The downloaded excel will be produced for the current selected "Software" toggle setting.

Processing Data with BIO_CYCLE

Users can upload data to the BIO_CYCLE web portal to produce the statistics described here. Results are generated for all included symbols in the user provided file at 3 period searches (8, 12, 24). The user can quickly view trends using these provided symbols under the "Visualization" tab shown below. Distribution of the previously described statistics can be examined in histograms displayed under the "Histogram" tab as shown below.

File must be a tab separated file (*.tsv) with a single ID in the first column followed by the molecular concentrations at each timepoint. An example file format is provided in the link below. BIO_CYCLE can handle variable numbers of replicates, uneven timepoints, and missing replicates (as long as each row has at least one value per timepoint).

EXAMPLE DATA FORMAT

ID ZT_0_REP_1 ZT_0_REP_2 ZT_4_REP_1 ZT_4_REP_2
Per1 4.25 3.08 9.17 8.90
Per2 3.45 na 9.50 9.93
Per3 1.40 1.53 10.70 10.55
Cry1 4.35 5.78 14.87 12.21

BIO_CYCLE Results

BIO_CYCLE is a Neural Network based approach which predicts rhythmicity in biological species. It is the default method used by CircadiOmics. For information on provided statistics and how to upload user data follow the links.

Visualization Of User BIO_CYCLE Data

Histogram Analysis Of User BIO_CYCLE Data

Metabolic Atlas

Is currently being developed to examine metabolomic networks through identification of correlated trends in the metabolome datasets found inside CircadiOmics.

Further Help

For further help, contact nickceglia@gmail.com