Research Institute at The Children's Hospital of Philadelphia

Welcome to KnowYourCG

    An automated discovery tool for discovering hidden biological and technical links

    KnowYourCG scans your CpG set against a large collection of knowledgebases for set enrichment, revealing the functional implications of DNA methylation data.

    1

    Define your query set

    Example
    MM285 ID list 468 probe IDs, as text Load Download
    or
    How to make a .cg (YAME docs)
    Examples
    MM285 .cg the same 468 probes, packed as a binary .cg Load Download
    hg38 whole-genome .cg 17,408 CpGs drawn mostly from H3K27me3 sites Load Download
    2

    Choose platform and databases

    Common groups are preselected. Hover a group for details.

    Select a platform to see its database groups.

    By default every probe on the array is the background. Check a restriction to count only those probes, in your query and in the background alike, so that enrichment is not driven by probe type, sex chromosomes or unreliable probes. Checked restrictions combine: "cg probes only" + "Autosomes only" tests against autosomal cg probes. Autosomal cg probes are preselected for .cg uploads. Probe masks and chromosomes come from InfiniumAnnotation (the SeSAMe recommended masks).

    Select a platform to see the restrictions it offers.

    Run it on the command line

    Processing a lot of data? The same test runs locally with kycg, with no size limits, many queries at once.     
    # install kycg and yame
conda install -c zhou-lab -c conda-forge kycg yame

# fetch the knowledgebases for your array
kycg fetch -f EPIC

# a probe ID list, one ID per line
kycg test -p EPIC -m EPIC:CGI,ChromHMM,HM hits.txt

# a binary .cg query: pack one 0/1 per probe, in the array's probe order
yame pack -f b hits01.txt hits.cg
kycg test -m EPIC:CGI,ChromHMM,HM hits.cg

# lots of data: many queries in one run, one results table
kycg test -m EPIC:CGI,ChromHMM,HM -o results.tsv samples.cg more.cg

# universe restriction: -u keeps only the rows set in a record; repeat to combine
# (cg probes here; any 0/1 .cg over the array's rows works, e.g. your own mask)
kycg test -m EPIC:CGI -u ~/.local/share/yame/EPIC/KYCG/ProbeType.cm:cg hits.cg

    See the KnowYourCG docs for all options and the YAME docs for packing .cg files.