Before running TRAP

Workflow of TRAP is as follows :
1. Using Tophat and Cufflinks software, TRAP maps reads and estimates abundances. (gff file is used as Cufflinks input)
2. TRAP extracts gene expression values from Cufflinks results and starts time-series analysis.
3. Analysis of TRAP utilizes pathway information and gene interaction information (eg. activation or inhibition between genes) provided by KEGG.

You can start TRAP from step 2 but it needs annotated gene expression as an input.
(usually a tab-delimited file with gene symbol in one column and expression value in another)
If your expression file is not same as Cufflinks result format, please use TRAP-web or contact me at keialk@snu.ac.kr.

In step 3, TRAP makes use of pathway information as a form of KGML file provided by KEGG database.
This enables TRAP to estimate cascading effects between genes in a pathway based on public information, which is different from inferring pathway without any previous knowledge.
Check if KEGG provides pathway information of your species of interest here, and check if the annotation you used for gene expression estimation is same as that of KEGG by http://rest.kegg.jp/list/***, where *** should be an organism code in the above link.
If KEGG does not support your species of interest but you have your own list of genes or pathways to analyze, it is also possible to make your own KGML files.

How to run TRAP

TRAP - Please refer to DOWNLOAD page.
TRAPweb - Please refer to instruction (click the icon '?') in TRAP-web page.

Result File Formats

OneTime_N_pathway.txt TimeSeries_pathway.txt	This file contains a list of pathways ranked by pG_FDR (or pORA_FDR). pG_FDR is a combined p-value of pORA and pPERT with FDR correction. pNDE and pPERT is calculated by ORA and SPIA algorithm, respectively. If a pathway does not have any interaction between genes, its representative p-value is pORA_FDR, not pG_FDR. Also, all the values related to interaction such as tA, pPERT, pG, pG_FDR will not be provided.
OneTime_N_color.txt	This file contains genes named as their KEGG ID and their color given by TRAP. Genes are colored as red (up-regulated) or blue (down-regulated). There are 6 steps of gradation including red/blue and white. You can put the text file as an input of KEGG search&color pathway mapper.
OneTime_N_DEG.txt TimeSeries_DEG.txt	This file contains DEGs using user-defined cutoff. If there are two replicates for each sample, representative FPKM for a gene is calculated as arithmetic mean and for three or more replicates, median is used.
Clustering_cluster.txt	This file contains all possible clusters by direction labeling and their p-values. Calculation of p-value for cluster is based on the permutation based approach used in STEM.
Clustering_gene.txt	This file contains a list of genes belonging to each cluster.
Clustering_pathway.txt	This file contains result of pathway analysis by ORA for each cluster. It tests if the ratio of genes (from a certain cluster) in a pathway is significantly big compared to the size of a cluster.
TimeSeries_pathway.png	This file is a diagram of the pathway network. Each node represents a pathway and edge exists if there are common genes between pathways. Node size is proportional to the number of genes in the pathway and node color is based on the p-value.