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PRIMA  v1.0 (for Windows)

 PRIMA (PRomoter Integration in Microarray Analysis) is a program
 for finding transcription factors (TFs) whose binding sites are
 enriched in a given set of promoters. PRIMA is typically used for
 the analysis of large-scale gene expression data. Microarray
 ('DNA chip') measurements point to alterations in gene expression
 levels under varying biological conditions, but they do not,
 however, directly reveal the transcriptional networks that underlie
 the observed transcriptional modulations. PRIMA is aimed at the
 identification of TFs that take part in these networks. The basic
 biological assumption is that genes that are co-expressed over
 multiple biological conditions are regulated by common TFs, and
 therefore are expected to share common regulatory elements in their
 promoters. By utilizing human genomic sequences and models for
 binding sites (BSs) of known TFs, PRIMA identifies TFs whose BSs
 are significantly over-represented in a given set of promoters.

 This version of PRIMA is a Windows console application. Read below
 on how to run PRIMA.

 Written by Chaim Linhart, Ran Elkon and Roded Sharan
         under the supervision of Prof. Ron Shamir,
         Tel-Aviv University, ISRAEL,
         2002-2003.

 Copyright C. Linhart, R. Elkon, R. Sharan, R. Shamir,
         Tel-Aviv University, 2003.

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CONTACT

 For support please contact chaiml@post.tau.ac.il.

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REQUIREMENTS

 Hardware requirements: Pentium-III PC, 800MHz, 256MB RAM,
                        300MB free disk-space.
 PRIMA was compiled and tested under WinNT 4.0 using MS VC++ 6.0.
 Some parts of PRIMA were written in Perl and compiled using
 the perl2exe tool (see http://www.indigostar.com/perl2exe.htm).

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CONTENTS

 This zip archive contains the following files:
   README.txt                - this file
   Prima_v1.0.exe            - the PRIMA executable
   coverageProb.exe, runProfile.exe - additional executables used by PRIMA
   HumanPromoters13K.dat     - putative promoters (1200bp upstream the TSS) for
                               12,981 human genes, downloaded from NCBI
   bg.all.13K.llid           - a list of the id's of the above 13K genes, used
                               as the background set for PRIMA runs
   tar.hcc.568.llid          - a list of 568 genes that are periodically expressed
                               during the human cell-cycle (Whitfield et al., 2002)
   tar.hcc.5_phases.568.llid - the above list partitioned into the 5 phases
                               of the cell-cycle
   matrix_E2F.dat            - a sample TF file with two PWMs (TRANSFAC format)
   output.txt                - a sample output file (see "USAGE")

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USAGE

 PRIMA receives three input files:
 (1) PWMs - transcription-factor PWMs in TRANSFAC format (a sample
     file, 'matrix_E2F.dat', is supplied in this zip archive);
 (2) BG set - a list of LLid's (LocusLink gene id's) used as the
     background set;
 (3) Target set - a list of LLid's used as the target set. The file
     may contain several target sets, see e.g., 'tar.hcc.5_phases.568.llid'.

 PRIMA reads the BG and target sets promoters from the file
 'HumanPromoters13K.dat', which contains promoter sequences of
 length 1200bp for 12,981 human genes (data downloaded from NCBI).
 For each PWM in the PWMs file, PRIMA evaluates its enrichment
 (over-representation) in the target set by comparing the number
 of putative binding-sites, or hits, in the target set and in
 the background (BG) set. The enrichment is computed using a
 hyper-geometric score, and its p-value is printed. The score is
 accurate only if the target set is a subset of the BG set.

 PRIMA receives its input parameters using a Unix-style list of flags.
 For a description of all available command-line parameters, run:
   Prima_v1.0.exe -h

 A typical execution of PRIMA would look like this:
   Prima_v1.0.exe -pwm matrix_E2F.dat -bg bg.all.13K.llid -tar tar.hcc.568.llid
 The file 'output.txt' contains PRIMA's output for the above example.
 On a Pentium-4 1.4GHz PC, the above run takes approximately 20 minutes.


 Important notes:
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 * PRIMA could consume a lot of memory. It's recommended that you run
   it on a machine with 256MB RAM or more.
 * To run PRIMA, open a DOS command window, enter the folder in which
   you saved the PRIMA files (using the "cd" command, e.g., "cd C:\Prima"),
   and then run PRIMA, as described above.
 * PRIMA creates large temporary files during its execution, which is
   why you need up to 300MB of free hard-disk space. The names of these
   files have the ".tmp" suffix. Normally, PRIMA removes these files
   automatically. However, in some abnormal situations, these files
   might not be deleted. If you detect such files in your PRIMA folder
   (while you're NOT running PRIMA), delete them.
 * As mentioned above, the enrichment score computed by PRIMA is
   accurate only if the target set is a subset of the BG set. Moreover,
   neither set should contain a gene more than once (i.e., make sure
   each LLid appears only once in the target and BG sets).
 * The algorithm and score used in PRIMA are described in the paper
   cited below (Elkon et al., 2003).

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HOW TO CITE THIS WORK

 Elkon, R., Linhart, C., Sharan, R., Shamir, R., and Shiloh, Y.,
 "Genome-wide In-silico Identification of Transcriptional Regulators
  Controlling Cell Cycle in Human Cells", 
 Genome Research, Vol. 13(5), pp. 773-780, 2003.

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