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GO enrichment analysis for non-model species-error #2

Open sekhwal opened 3 years ago

sekhwal commented 3 years ago

Hi, I am trying to perform GO enrichment analysis for non-model species. For that I used BiNGO at Cytoscape. I tried to download a gaf file (annotation file) as reference from the GO database and and updated it as the following manner:: However, once I hit the start BiNGO button, it shows "Could not load annotation file. Unrecognized file format." Please help me to figure out the issue.

(curator=GO) type=process) 0003673 = Gene_Ontology 0006854 = cytidine metabolism 0046088 = cytidine biosynthesis 0046089 = cytosine biosynthesis 0042882 = L-arabinose transport 0042883 = L-cysteine transport

Input File: (list of genes and GO terms) SE_06589 = 0006854 SE_04589 = 0006081

Picture1

ERROR: Could not load annotation file. Unrecognized file format.

radoslav180 commented 3 years ago

Hi sekhwal, I am not BiNGO developer, but I used BiNGO. As I see there are a few issues. When you paste genes from text then you should paste them as follows: gene1 gene2 gene3 . . . geneN The second issue is gene ID. You use dbSuper IDs (correct me if I wrong), but BiNGO does not support them by default. The third issue is incorrect format of the annotation file. The header should be something like this: (species=Homo sapiens) (type=Biological Process) (curator=GO).

Best regards, Radoslav.

sekhwal commented 3 years ago

Hi, Thank you for your reply. I heard back from BiNGO developer team and suggested the following tutorial. Therefore, I used my input data as the following manner and tried in many ways but not getting BiNGO results. I prepared custom ontology file with Gene IDs and GO terms (L = 1) information. Please let me know if you have idea to figure out the issue.

Input data::

Annotation file

(species=Sequoiadendron giganteum)(type=Biological Process)(curator=GO) SEGI_09259 = 0008152 SEGI_09259 = 0003824 SEGI_29666 = 0050896 SEGI_13597 = 0008152

Ontology file

(curator=GO)(type=all) 0008152 = molecular_function (L =1) 0003824 = anticoagulant (L = 1) 0050896 = antifreeze (L = 1) 0008152 = molecular_function (L =1)

radoslav180 commented 3 years ago

Hi, The structure of ontology file should be as follows: (curator=bingo)(type=namespace) 35203 = regulation of lamellocyte differentiation[isa: 45610 48580 ] 70407 = oxidation-dependent protein catabolic process[isa: 19941 ] 1 = mitochondrion inheritance[isa: 48311 48308 ] 35202 = tracheal pit formation in open tracheal system[isa: 48646 7424 ] 2 = mitochondrial genome maintenance[isa: 7005 ] 35201 = leg disc anterior/posterior lineage restriction[isa: 48099 35200 ] 3 = reproduction[isa: 8150 ] You may use go.obo file instead.