agriGO - analysis tool

Amphibia group analysis

1. Select analysis tool:

Singular Enrichment Analysis (SEA)

Parametric Analysis of Gene Set Enrichment (PAGE)

Cross comparison of SEA (SEACOMPARE)

Customized comparison

Reduce + Visual Gene Ontology (REVIGO)

PAGE method is using Central Limit Theorem in statistics, this method is simple and efficient. Different to SEA, it takes expression level into account, and can deal with a long list of genes/probesets.

2. Select the species:

<allowed ID types in Arabidopsis>
TAIR locus ID: AT3G34250
TAIR alias ID: ACL3
TAIR transcript ID: AT3G34250.1
GenBank ID: AAP50233.1
DDBJ ID: BAB11514.1
EMBL ID: CAA18188.1
UniProt ID: Q9LYA9
RefSeq Peptide ID: NP_564434
PDB ID: 2zsi_B
Affymetrix ATH1 Genome Array (GPL198): 267636_at
Affymetrix 8K Genome Array (GPL71): 16876_at
Operon Array v3, Meyerowitz (GPL2810): A021028_01
Agilent 3 Oligo Microarray (GPL2871): A_84_P69894
OAR27K array, Yale University (GPL988): 3243009

No your ID? Try BLAST4ID

3. Submit your data

Query list [ Example 1 Example 2 ]

Set first row as header
Numerical value is log2 transformed
Or upload file (Limited to 4MB)

For PAGE analysis, at least two columns are required in submit data. One column for entity names, one or more than one columns for numerical value. Each line should have same columns. The numerical value is fold change(FC) or log2-transformed FC value (latter preferred) of the entity's expression under different condition. If you do not have expression data, then SEA may be the alternative choice. 
Note: If you want set your first row as the header in your result, you should check 'Set first row as header'. And if your value is log2 transformed, you should check 'Numerical value is log2 transformed'. Please be very careful to this !!!

Amphibia group analysis

1. Select analysis tool:

Singular Enrichment Analysis (SEA)

Parametric Analysis of Gene Set Enrichment (PAGE)

Cross comparison of SEA (SEACOMPARE)

Customized comparison

Reduce + Visual Gene Ontology (REVIGO)

2. Select the species:

3. Submit your data

4. Advanced options (optional):