REDUCE Suite

Transfactivity is a utility program that performs multiple-linear regressions of measurements (gene expression or binding data) against affinities. As with AffinityProfile, the affinities can be deduced either from a list of PSAMs or IUPAC motifs, or a single PSAM (-psam=one_PSAM_file) or an IUPAC motif (-motif=one_IUPAC_motif) specified directly on the command-line. The PSAMs can be from a MatrixREDUCE or MotifREDUCE run, or a collection of pseudo-PSAMs from literature (as in the $REDUCE_SUITE/data/PSAMs/ directory).

Transfactivity [options] -sequence=seqfile -measurement=measfile \
                         -psam=one_PSAM_file | -psam_list=list_of_PSAMs |
                         -motif=one_IUPAC_motif | -motif_list=list_of_motifs

  Required parameters:
    -sequence=seqfile      --- sequence file in FASTA format
    -measurement=measfile  --- measurement data file in tab-delimited format
    -psam=one_PSAM_file    --- file name of one PSAM
    -psam_list=list_of_PSAMs --- file name containing a list of PSAMs
    -motif=IUPAC_motif     --- one IUPAC motif
    -motif_list=list_of_motifs --- file name containing a list of IUPAC motifs

  Optional parameters:
    [-damid]               --- short-hand form for -motif=GATC
    [-output=dir_name]     --- path to the output directory (./)
    [-copy]                --- copy CSS, JavsScript and image files to the above
                               output directory to make the HTML self-contained
    [-univariate]          --- switch to run univariate fit only
    [-acgt]                ---  i.e., -motif_list=$REDUCE_SUITE/data/acgt.dat
    [-resid_file=file_name] --- name of residuals
    [-strand=integer]      ---  1 |+1 |F | L for leading strand;
                                2 |+2 |B     for both strands;
                               -1 | R |C     for reverse complementary;
                                   with -motif, default to leading strand
                                   with -psam, default to PSAM setting
    [-runlog=[stderr|stdout|file]]
                           --- direct running diagnostics message to stderr,
                               stdout or a specific file (stderr)
    [-help]                --- print out this help message

Usage:
    Transfactivity \
       -measurement=$REDUCE_SUITE/data/mRNA_expression/Spellman1998AlphaTimeCourse.tsv \
       -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
       -psam_list=psams.list

    Transfactivity \
       -measurement=$REDUCE_SUITE/data/mRNA_expression/Spellman1998AlphaTimeCourse.tsv \
       -sequence=$REDUCE_SUITE/data/sequence/YeastUpstream.fasta \
       -motif_list=motifs.list

Note:

---

Given a directory that contains all the PSAMs one is interested in, the PSAM-list file can be conveniently generated with the Perl script "psamdir2list". This trick applies to Transfactivity here as well as to AffinityProfile.

For example, the PSAM list in $REDUCE_SUITE/examples/Transfactivity/MacIsaac.list was generated as:


As another example, the Jaspar PSAM list can be generated as: