Workflows and Reports Tab

Analyze Single Experiment Workflow

• The analyze single experiment workflow allows one experiment to be tested. Activate the an experiment with desired thresholds applied and select Analyze Single Experiment from the Workflows & Reports list.

• Confirm Network object count and threshold settings and click Apply.

• Results are returned by ontology, statistics are -log(pValue) (1.3 = 0.05)

• Results can be examined by clicking on the name. See Legend for more information about maps and networks. Note: network objects included in filtered sets display expression results in image.

• Different results link to different types of data.

  • Pathway maps are nice interactive maps

  • Process networks and network statistics produce editable network maps.

  • GO Processes produce lists that can be used to draw networks.

  • Diseases link to disease pages.

Enrichment Analysis Workflow

• This workflow requires at least 2 active experiments. Activate all 3 ColonMet experiments and refresh the browser page to confirm.

• Select the Enrichment Analysis link to launch the workflow. Ensure the correct experiments are activated and click Next.

• Fold change, p-value signal directionality can be adjusted on the next page. NOTE: the number of Network objects that meet threshold criteria are indicated. Clicking Apply launches the analysis.

• Results are returned by ontology, statistics are -log(pValue) (1.3 = 0.05)

• Results can be examined by clicking on the name. See Legend for more information about maps and networks. Note: network objects included in filtered sets display expression results in image.

• Different results link to different types of data.

  • Pathway maps are nice interactive maps

  • Process networks produce editable network maps.

  • GO Processes produce lists that can be used to draw networks.

  • Diseases link to disease pages.

Compare Experiments Workflow

• This workflow requires at least 2 active experiments. Activate all 3 ColonMet experiments and refresh the browser page to confirm.

• Select the Compare Experiments link to launch the workflow. Ensure the correct experiments are activated and click Next.

• Fold change, p-value signal directionality can be adjusted on the next page. NOTE: the number of Network objects that meet threshold criteria are indicated. Clicking Apply launches the analysis.

• Genes passing thresholds in each experiment are compared and grouped in 3 categories:

1. Unique

2. Similar - present in more than one list

3. Common - present in all lists

• Results are returned by ontology, statistics are -log(pValue) (1.3 = 0.05)

• Results can be examined by clicking on the name. See Legend for more information about maps and networks. Note: network objects included in filtered sets display expression results in image.

• Different results link to different types of data.

  • Pathway maps are nice interactive maps

  • Process networks and produces editable network maps.

  • GO Processes produce lists that can be used to draw networks.

  • Diseases link to disease pages.

• Histograms can be sorted according to statistics

1. Statistically significant

2. Deferentially effected

3. Similarity by

4. Particular

• Histogram are interactive, network statistics panel reports results.