Result interpretation

The output

1. Input data

This section is a reminder of the parameters or settings you have submitted to run the analysis. The two lists analysed can be downloaded as a text file, even when the genome (TFBS or miRNA) or your annotations comparison have been chosen.

Input data

2. Summary

This section shows the number of genes annotated to each database in each list.

  • Gene list: contains three elements, the number of genes in your gene list annotated in the database over the total number of genes remaining in your gene list after the duplicates management, a percentage of genes in your gene list annotated in the database and the ratio of regulators per gene.
  • Genome: the same structure explained above but applied to the whole genome (TFBS or miRNA) or Your Annotations after the duplicates management.


Summary

3. Significant results

The number of significantly enriched regulatory elements is indicated in this section. We consider a significant enrichment after correcting the results by a multiple testing correction method. Enrichment p-values are corrected applying the False discovery rate (FDR) method (Benjamini et al., 1995; Storey andTibshirani, 2003). The threshold of signification applied to the correction has been set to 0.05.

The table provided summarizes the information about the enrichment test for each of the significant regulatory elements that have an Adjusted p-value < 0.05. The table table is originally sorted by adjusted p-value and can be sorted up and down by clicking in any of the other column headings. When the number of significant results in a table is higher than five, results are split into different pages. You can move forward or backward in the page list using the arrow buttons.

Significant results

The following fields are described in the results table:

  • Term: name or ID of the regulatory element.
  • List1 annotateds: number of genes in your gene list that are regulated by this regulatory element.
  • List1 unannotateds: number of genes in your gene list that are not regulated by this regulatory element.
  • List2 annotateds: number of genes in the genome or in your annotation that are regulated by this regulatory element.
  • List2 unannotateds: number of genes in the genome or in your annotation that are not regulated by this regulatory element.
  • Odds ratio (log e): the odds ratio is a way of comparing whether the probability of a certain event is the same for two groups, the sign of it will give us the idea of which of the lists is enriched for this regulator. When the log e (odds ratio) is positive your gene list is enriched for this regulator, when the log e (odds ratio) is negative the enrichment is related to the genome or your annotation.
  • pvalue: unadjusted p-value from Fisher's exact test.
  • Adjusted pvalue: adjusted pvalue from Fisher's exact test, after correcting for multiple testing, using the FDR procedure of Benjamini & Hochberg. Keep in mind to use this p-value instead of the unadjusted one as RENATO is performing a great number of test simultaneously and the error rate must be corrected.

A downloadable text file is provided containing the complete results for the significant regulators. This file contains a similar structure as the table:

  • Term: name or ID of the regulatory element.
  • term size: number of genes in the genome or in your annotation that are regulated by this regulatory element.
  • term size in genome: number of genes in the genome or in your annotation that are regulated by this regulatory element.
  • List1 positives: number of genes in your gene list that are regulated by this regulatory element.
  • List1 negatives: number of genes in your gene list that are not regulated by this regulatory element.
  • List1 percentage: percentage of genes in your gene list that are regulated by this regulatory element.
  • List2 positives: number of genes in the genome or in your annotation that are regulated by this regulatory element.
  • List2 negatives: number of genes in the genome or in your annotation that are not regulated by this regulatory element.
  • List2 percentage: percentage of genes in the genome or in your annotation that are regulated by this regulatory element.
  • list1 positive ids: list of genes in your gene list that are regulated by this regulator.
  • list2 positive ids: list of genes in the genome or in your annotation that are regulated by this regulator.
  • Odds ratio (log e): the odds ratio is a way of comparing whether the probability of a certain event is the same for two groups, the sign of it will give us the idea of which of the lists is enriched for this regulator. When the log e (odds ratio) is positive your gene list is enriched for this regulator, when the log e (odds ratio) is negative the enrichment is related to the genome or your annotation.
  • pvalue: unadjusted p-value from Fisher's exact test.
  • Adjusted pvalue: adjusted pvalue from Fisher's exact test, after correcting for multiple testing, using the FDR procedure of Benjamini & Hochberg. Keep in mind to use this p-value instead of the unadjusted one as RENATO is performing a great number of test simultaneously and the error rate must be corrected.

4. All results

This section contains a downloadable individual text file containing all results for all significant and not significant regulators. This file follows the same structure described above.

5. Annotation files

A downloadable file containing the identifier-regulator correspondence. If a gene is annotated to several labels, each of the annotations is listed in a separate line. These lists can be used as an input annotation file in the RENATO Your Annotations mode.

Network viewer

By default, the Network viewer displays the regulatory elements that have obtained a significant p-value (<0.05) in the test ( nodes), showing as targets the genes introduced by the user ( nodes). This visualization is completely interactive and contains many functionalities. Take a look at at the Network viewer tutorial for further details on its usage.

Network

Interpretation

When significant results are obtained, we can suppose that there is one or several regulatory elements behaving different when comparing groups. The list of genes included in the analysis have pointed to a significantly over-represented set of common regulators to these genes. The interpretation of the results will be different in the case of TFs (transcription factors) and miRNAs given that (generally) the first are positive regulators and the latter are negative regulators.

TFs generally bind to the promoter region of their target genes to assist and promote the transcription. miRNAs, on the other hand, bind to transcript products preventing them from being translated. Significant TF and miRNAs can be pointed to be responsible for the differential expression of the genes observed in the list. We must take special care in the interpretation of over-expressed or under-expressed genes in a functional analysis. In the case of TFs, if we are working with the list of over-expressed genes, the significant results makes reference to active TFs in one condition with respect to the other; while significant results of under-expressed genes makes reference to inactive TFs. In miRNAs, significant results of over-expressed genes will point to inactive miRNAs, while significant results of under-expressed genes will point to active miRNAs when comparing conditions. The following table summarizes the result interpretation:

TFs miRNAs
Over-expressed genes
Under-expressed genes
result_interpretation.txt · Last modified: 2012/05/03 15:33 by mbleda
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