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INCATools / fantom5-ontology

ontology categorizing samples from FANTOM5 project
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11590-120G6 should be Alveolar Epithelial Cells, donor2 #9

Closed cmungall closed 9 years ago

cmungall commented 9 years ago

Hi Chris, Terry,

In the FANTOM5 sample ontology annotation, sample 11590-120G6 is listed as "Renal Glomerular Endothelial Cells, donor2"; this is the entry in ff-phase2-140729.obo.txt:

[Term] id: FF:11590-120G6 name: Renal Glomerular Endothelial Cells, donor2 namespace: FANTOM5 comment: Previously: Alveolar Epithelial Cells, donor2 subset: phase1 subset: phase2 subset: update022 is_a: EFO:0002091 ! biological replicate is_a: FF:0000153 ! human renal glomerular endothelial cell sample

However, the .bam file names still refer to "Alveolar Epithelial Cells, donor2": ... Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.ctss.bed.gz Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.bam Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.bam.bai Alveolar%20Epithelial%20Cells%2c%20donor2.CNhs12084.11590-120G6.hg19.nobarcode.rdna.fa.gz ... on the FANTOM5 website; and also in the sRNA data in UPDATE_023: /analysisdata/mirrors/F5_file_current/UPDATE_023/f5pipeline/human.primary_cell.sRNA/Alveolar%20Epithelial%20Cells%2c%20donor2.SRhi10002.11590-120G6.hg19.CTTGTA.bam.bai /analysisdata/mirrors/F5_file_current/UPDATE_023/f5pipeline/human.primary_cell.sRNA/Alveolar%20Epithelial%20Cells%2c%20donor2.SRhi10002.11590-120G6.hg19.CTTGTA.bam

Marina checked the expression for some genes to verify the expression patterns of the two samples below (Renal vs Aveolar cells), and based on that we think the .bam file names are correct. (Expression of sox7 is enriched in renal cells (zero in alveolar), vice versa expression of elf3 is high in alveolar cells and null in renal cells).

I am wondering, since the entry in the ontology file has the comment "Previously: Alveolar Epithelial Cells, donor2", if you know what happened to this sample, and should the ontology file be corrected?

Thanks in advance, -Michiel

cmungall commented 9 years ago

From Michiel: I couldn't find these three entries anywhere: FF:11583-120F8 ! hair follicle germinal matrix cell FF:11585-120G1 ! inner root sheath cell-FF:11585-120G1 FF:11589-120G5 ! smooth muscle cell of intestine I am guessing that in the end they were not used in FANTOM5.

I checked these; they all seem to be OK: FF:11582-120F7 ! Melanocyte - dark, donor2 FF:11584-120F9 ! Hair Follicle Outer Root Sheath Cells, donor2 FF:11586-120G2 ! Fibroblast - Lymphatic, donor2 FF:11587-120G3 ! Esophageal Epithelial Cells, donor2 FF:11588-120G4 ! Smooth Muscle Cells - Esophageal, donor2 FF:11591-120G7 ! Bronchial Epithelial Cell, donor2 FF:11592-120G8 ! Smooth Muscle Cells - Bronchial, donor2 FF:11593-120G9 ! Smooth Muscle Cells - Tracheal, donor2 FF:11594-120H1 ! Renal Glomerular Endothelial Cells, donor2

This is the one that needs to be fixed to "Alveolar Epithelial Cells, donor2" FF:11590-120G6 ! Renal Glomerular Endothelial Cells, donor2 Note that "Renal Glomerular Endothelial Cells, donor2" also occurs in the list above.