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Signatures
A Signature is a set of genes with some common characteristic or function. For example, the set of genes involved in the process of coagulation.
Alternately, signatures can describe changes in gene expression between two conditions. For example, a signature could describe "When comparing dendritic cells 4 hours post LPS stimulation, Genes A, B, C, D ... are up-regulated and Genes X, Y, Z ... are down-regulated."
A great resource for signatuers is the MSigDB, by the Broad Institute
By using the "Search Gene Sets" dialog, many signatures can be downloaded at once in the .gmt file format, which can be input directly into VISION without modification.
Yes, you can create your own signatures. See the section below for information on correctly formatting the signature file.
List of gene signatures
Text, tab-delimited Genes should match the row labels in the input data matrix (matching is case insensitive)
One gene per line (each signature has many lines)
<Signature Name> TAB <Signature Sign> TAB <Gene Name>
<Signature Sign> can be either "plus", "minus", or "both" if it's unsigned.
Alternately, you can just omit the second column and all genes will be treated as unsigned.
Example:
| Lin-neg_cell_vs_NKT_cell | plus | TEK |
| Lin-neg_cell_vs_NKT_cell | plus | AGPAT5 |
| Lin-neg_cell_vs_NKT_cell | plus | HSPA4L |
| Lin-neg_cell_vs_NKT_cell | plus | FAM126A |
| Lin-neg_cell_vs_NKT_cell | minus | UBR1 |
| Lin-neg_cell_vs_NKT_cell | minus | CYSLTR2 |
| Lin-neg_cell_vs_NKT_cell | minus | ZNF205 |
| Lin-neg_cell_vs_NKT_cell | minus | UBXN11 |
| B_cell_vs_CD4T_cell | plus | RAB39 |
| B_cell_vs_CD4T_cell | plus | EVI2B |
| B_cell_vs_CD4T_cell | plus | GALNS |
| B_cell_vs_CD4T_cell | plus | CRIP3 |
| B_cell_vs_CD4T_cell | plus | HES6 |
| B_cell_vs_CD4T_cell | plus | HMGXB4 |
| ... | ... | ... |
One signature per line, (however "plus" and "minus" genes are split into two lines) Each line:
<Signature Name> TAB <Signature Description> TAB <Gene1> TAB <Gene2> … (etc)
The signature description is ignored by VISION: that column just exists so the format conforms to the standard .gmt format.
To denote signature signs, use two lines to show the signature, with the "plus" genes in one and the "minus" genes in the other. Add "_plus" to the signature name on the line with the "plus" genes and "_minus" to the signature name on the line with the "minus" genes.
Example:
| MEMORY_VS_NAIVE_CD8_TCELL_plus | GSE16522P | RHOC | OFD1 | MLF1 | ... |
| MEMORY_VS_NAIVE_CD8_TCELL_minus | GSE16522 | PTPRK | S100A5 | IL1A | ... |
| BCELL_VS_LUPUS_BCELL_plus | GSE10325 | OXT | KCNH2 | BTBD7 | ... |
| BCELL_VS_LUPUS_BCELL_minus | GSE10325 | VAMP5 | WSB2 | CCR2 | ... |