The gene-lists directory in this repository contains all the files used to prepare the lists of filtered-out genes.
- The complete list of Homo sapiens genes supported by CAP can be found in homo_sapiens.csv.
- The list of genes ignored by CAP when the gene filtering flag is enabled is available in filtered_out.csv.
Gene filtering is based on filtering by locus group and locus type terms from the HGNC Statistics & files and a curated list of BCR and TCR genes.
CAP automatically filters out genes which are often over-expressed but biologically non-informative. The following genes are filtered out when reporting differentially expressed genes displayed on the heatmap:
Mitochondrial genes
- Genes from from genenames.org where “Chromosome == Mitochondrial”
- All genes where the “Gene group name” contains the word “mitochondria”
Mitochondrial pseudogenes
- All the pseudogenes associated with the genes selected in the mitochondrial genes section
- Example: For MT-RNR2 we filter “MT-RNR2 like 12 (pseudogene)”
Ribosomal genes
- All genes where the “Locus type” contains the word “ribosomal”
Ribosomal pseudogenes
- All pseudogenes, subset by “Locus Type == pseudogene,” that contain the word “ribosomal” in the “Approved name” column
lncRNA genes
- All genes where the “Locus type” contains “RNA, long non-coding”
lncRNA pseudogenes
- All the pseudogenes associated with the genes selected in the lncRNA genes section
- Example: For RN7SKP1, “RN7SK pseudogene 1” is filtered
TCR genes
- All the genes listed in TCR genes
- Excluding:
- TRAV1-2 (MAIT marker)
- TRGV9 and TRDV2 (circulating gdT marker)
BCR genes
- All the genes listed in BCR genes