Candidates Page Overview

The Candidates page typically has three tabs: Transcriptome, Transcriptome Pairwise, and Genome.

Transcriptome Tab

The Transcriptome tab contains comparative expression data for your sample groups, one row per transcript.

You can sort the data in a column in ascending or descending order by clicking on the column header. Each column has a search field to filter your data.

Column Breakdown

  • Gene – This is the gene name of the transcript. Click on the name to link to the transcript record at NCBI.
  • Transcript ID – The transcript identifier. Clicking the link takes you to this transcript in the UCSC genome browser.
  • Pathway – Annotations curated by expert biologists provided by the Reactome database. Version 49 annotates 7357 human genes in 1551 pathways.
  • Min P-value – This P-value is the minimum of all the pairwise P-values between groups, determined by a Welch’s t-test. Smaller values are more significant. P-values are corrected for multiple testing using the two-step adaptive method of Benjamini and Hochberg (2000).

Use the search box underneath the Min P-value column header to filter by p-value. For example, type “<0.05” to see rows with Min P-values less than 0.05.

  • Fold Change – The maximum pairwise fold change (ratio of expression) among the sample groups.

  • Expression Max – This is the highest expression value among all sample groups.

  • Differentially Expressed? – Value for a gene/transcript can be 1 (Differentially Expressed) or 0 (Not Differentially Expressed). A gene is considered differentially expressed if:

    • The sum of the highest and lowest expression values is greater than or equal to a cutoff of 1 rpkm.
    • The fold change is greater than or equal to the value selected in the “Min Fold Change” column (2, 5, 10 or blank).

Example: For the gene MIR3652:

  • Highest expression = 11.29

  • Lowest expression = 4.67

  • 11.29 + 4.67 = 15.96 > 1 (criteria met)

  • Fold Change = 2.42 (criteria met when Min Fold Change is 2).

  • Expression String – Search for genes highly expressed in some sample groups but expressed at a low level in others. The expression string consists of 1’s and 0’s corresponding to sample groups.

  • Mean – The mean expression in rpkm for all samples within a group.

  • cv – The coefficient of variation (standard deviation divided by the mean for that sample group).

Transcriptome Pairwise Tab

The Transcriptome Pairwise tab is similar to the Transcriptome tab, with extra columns, Group A and Group B, allowing results for pairwise tests between one sample group and another. This is useful for comparing specific sample groups in experiments with multiple groups.