which file used for GO

Question

[fatimarasool135]

I have created the following output files by using the stringtie tool 1) Output GTF file containing the assembled transcripts by stringtie

2) A merged GTF file from all sample GTF

I am not sure which of the above file is used further for Gene Ontology by using tool DAVID or agriGO. The output of my file is as:-

Gene ID     Gene Name   Reference   Strand  Start   End     Coverage    FPKM        TPM
  NM_000451   SHOX        chrX        +       624344  646823  0.000000    0.000000    0.000000
  NM_006883   SHOX        chrX        +       624344  659411  0.000000    0.000000    0.000000
  ...

Am I supposed to pick the gene Id and expression value to find gene ontology results. Or there is something else I need to do.

[jean.elbers]

You need to perform differential transcript or differential gene expression to then potentially see if there are over-represented gene ontology terms or whatever your goal is. There is somewhat of a guide here http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#de if you want to use the developers' of StringTie tool called Ballgown.

[fatimarasool135]

Hi Jean elbers I did differential gene expression by hisat ,string-tie and ballgown. next, i have to do GO ,Singular Enrichment Analysis and KEGG. by using the tool agriGo.I do not know which gene list I have to provide as input to this agriGo tool.

[fatimarasool135]

list of genes is as

enter code here

feature id fc pval qval gene MSTRG.28632 0.341220148 1.95E-05 0.176761218 gene MSTRG.3615 5.155727198 2.21E-05 0.176761218 gene MSTRG.7507 0.251906716 2.22E-05 0.176761218

I have to use the database AgriGO....According to this tool, gene ids should be in format GenBank ID: AAP50233.1 DDBJ ID: BAB11514.1 EMBL ID: CAA18188.1 UniProt ID: Q9LYA9 RefSeq Peptide ID: NP_564434 PDB ID: 2zsi_B Wheat Affymetrix Genome Array: Ta.10183.2.S1_at but as you have seen mine data set gene list contain different gene ids ,how can I chang it