# Tox21 Concentration Response Browser

A browser designed to display concentration response data from Tox21.

A summary of activities are found in a related application, the [Tox21 activity profiler](/tox21-activity-browser/).

## Quick start

1. Paste a list of CAS numbers or other chemical identifiers in the "Compound loader". For example:

        83-79-4
        23541-50-6
        77-40-7

2. Select at least one pathway. For example, select:

        activation_p53
        agonism_ER/full

### Required inputs

#### Compound loader

please input either CAS or Tox21 ID. For chemical properties of compounds, please see the **Input compounds** tab.

#### Assays

Click + Control/Shift allows to select multiple assays. For the descriptions of assays, please see the **Assays** tab.

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### Other settings

#### Assay display modes

  * assay parallel
  * assay overlaid
  * assay parallel + cmpd overlaid

#### Assay readout options

  * run1/run2/run3: the result from different batches
  * cytotoxicity: counter-screen, cell viability assay, will only display when primary assay & run information are selected
  * BLA-signal/background: the signal channel or the background channel in two-channel assays (e.g. beta-lactamase assay)
  * AutoF-red/blue/green: counter-screen, the measurement type in the auto-fluorescence assay. Please combine with the primary assay option (autofluor\_hek293 or autofluor\_hepg2).

#### Line plotting options

  * raw: the normalized (against positive/negative control) data provided by NCATS
  * curvep: the Curvep results
  * Hill 4-point: the results based on 4-point Hill model provided by NCATS
    * cross outliers: the outliers are defined by Hill 4-point fitting results (may not work for certain data)
  * use color template for reporting (purple for the primary assay and black for the cell viaiblity assay)

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### Formatting and outputs
#### Resize plot image

  * width
  * height

#### Resize axes

  * Manually adjust x-axis (unit: log10(M))
  * Manually adjust y-axis (unit: %)

#### Save data

  * save melted data: the data can be used in other software (e.g., GraphPad Prism)
  * save plot: pdf file
  * If the assay does not have a PubChem AID in Assays tab, the data cannot be downloaded.

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### Tips

  * use the resize scroll bar if the size of the plot is not optimal
  * For a quick plot in powerpoint, use the right click "copy image" and paste into powerpoint or Paint for editing
  * For downloading results for many compounds (n > 20), click "save plot" or "save melted data" directly

### Known bugs

  * It does not recognize Tox21\_xxxxxx\_01 alone. Please add some other IDs.

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### Appendix

####  Purity information

<table class='table table-condensed table-striped'>
<thead>
<tr>
  <th>Purity Rating</th>
  <th align="center">Description</th>
</tr>
</thead>
<tbody><tr>
  <td>ND</td>
  <td>Not determined: analytical analysis in progress</td>
</tr>
<tr>
  <td>A</td>
  <td >MW confirmed, purity &gt;90%</td>
</tr>
<tr>
  <td>M</td>
  <td>Defined mixture, two or more components</td>
</tr>
<tr>
  <td>D</td>
  <td>Caution, purity &lt;50%</td>
</tr>
<tr>
  <td>Fns</td>
  <td>Caution, no sample detected, biological activity unreliable</td>
</tr>
<tr>
  <td>F</td>
  <td>Caution, incorrect MW, biological activiy unreliable</td>
</tr>
<tr>
  <td>Z</td>
  <td>MW confirmed, no purity info</td>
</tr>
<tr>
  <td>Ac</td>
  <td>Caution, low concentration, 5-30% of expected concentration value,   &gt;90% purity</td>
</tr>
<tr>
  <td>Fc</td>
  <td>Caution, very low concentration, &lt;5% of expected value, biological   activity unreliable</td>
</tr>
<tr>
  <td>B</td>
  <td>MW confirmed, purity 75-90%</td>
</tr>
<tr>
  <td>C</td>
  <td>MW confirmed, purity 50-75%</td>
</tr>
<tr>
  <td>I</td>
  <td>Two or more isomers detected</td>
</tr>
<tr>
  <td>Cc</td>
  <td>Caution, low concentration, 5-30% of expected concentration value, 50-75%   purity</td>
</tr>
<tr>
  <td>Bc</td>
  <td>Caution, low concentration, 5-30% of expected concentration value, 75-90%   purity</td>
</tr>
<tr>
  <td>W</td>
  <td>Sample withdrawn</td>
</tr>
</tbody></table>



### Release notes

*v1.1*

* new: add format for reporting
* new: add AR/full/run2 data
* changed: the purity table fixed

*v1.2*

* new: add CAR data
* changed: the purity table updated (v5a5)
* changed: show outliers default = FALSE (errors seen for some chemicals)
* changed: add more pubchem id for the assay annotation file

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### Contact

For further information, contact:

Jui-Hua Hsieh, Ph.D.
[Biomolecular Screening Branch](http://www.niehs.nih.gov/research/atniehs/labs/bmsb/toxico/staff/hsieh/index.cfm)