Signatures

What is a Signature?

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."

Where can I find signatures?

A great resource for signatuers is the MSigDB, by the Broad Institute

• http://software.broadinstitute.org/gsea/msigdb/

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.

Can I create my own signatures?

Yes, you can create your own signatures. See the section below for information on correctly formatting the signature file.

Acceptable Signature File Formats(file extension matters, see below)

List of gene signatures

Text, tab-delimited Genes should match the row labels in the input data matrix (matching is case insensitive)

Format A (File ends in .txt extension)

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
...	...	...

Format B (File ends in .gmt)

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	...