# 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.