SBSA Manual
This section will explain the all parameters in SBSA tool and how to operate and interpret results.
Input
Other Input
Options
Output
Input
Other Input
Options
Output
Fields in all output CSV files:
| Header | Meaning |
| Bind_seq | Oligo nucleotide sequence bound by a molecular regulator (TF/RBP). |
| Chromosome | Chromosome where a variant is located. |
| eQTL_gene (FineMapping) | Fine-Mapping-endorsed Ensembl gene ID of the regulated gene involved in the eQTL relation. |
| eQTL_gene (GTEx) | GTEx-endorsed Ensembl gene ID of the regulated gene involved in the eQTL relation. |
| eQTL_pos.prob (CAVIAR) | Posterial probability of eQTL association inferred by a "Fine Mapping" method (see more information on GTEx page). |
| Family_Conservation | TargetScan-defined miRNA conservation category (broadly conserved, conserved, poorly conserved, or “other”). |
| GTEx_variant | Variant ID as identified in GTEx datasets. |
| Host_gene | Symbol of the host gene whose body encloses or approximates the variant. |
| Location | Chromosome coordinate position of a variant. |
| MiRBase_ID | miRNA ID identified in miRBase. |
| miRNA_family | miRNA conservation family. |
| miRNAtarget.alt | miRNA target sequence in mRNA 3'-UTR carrying the variant. |
| miRNAtarget.ref | miRNA target sequence in mRNA 3'-UTR in the reference genome. |
| miRNAtarget_gene | Gene Symbol of the associated mRNA target of the miRNA. |
| miRNAtarget_geneID | Ensembl gene ID of the associated mRNA target of the miRNA. |
| Motif | ID of the plausible motif originating from the PWM file. |
| Motif_effect | Gain or Loss of the plausible motif resulting from the variant. |
| p.alt (FIMO) | P-value for the approximity between altered sequence (Seq.alt) and the PWM motif. |
| p.ref (FIMO) | P-value for the approximity between reference sequence (Seq.ref) and the PWM motif. |
| Region | Gene-relative classification of the genomic region enclosing the variant. Typical values include exonic, intronic, upstream, etc. |
| Regulator_context_expression | Contextual expression of plausible molecular regulator (TF/RBP), expressed as rank of the regulator in the GTEx transcriptomes. |
| Regulator_gene | Symbol of the molecular regulator that binds with the plausible motif. |
| Regulator_geneID | Ensembl gene ID of the molecular regulator that binds with the plausible motif. |
| Seed.alt | miRNA seed sequence carrying the variant. |
| Seed.ref | miRNA seed sequence in the reference genome. |
| Seq.alt | Altered sequence in parallel to Reference Sequence reflecting the variant in question. |
| Seq.ref | Reference sequence surrounding the variant location reflecting the reference genome. |
| Species_ID | Taxonomy ID of the species of the concerned miRNA. |
| Strand | Strandedness of the plausible motif or miRNA-related segments. |
| Tissue | The tissue concerned in Contextual expression or eQTL information. |
| Variant | Nucleotide change at a chromosome location as relative to the reference genome. |
| Variant_impact (CADD_phred) | Functional impact of the variant predicted by a sequence or conservation based algorithm. |