Frequently Asked Questions

  1. What is CressInt?

    CressInt is a web resource for exploring gene regulatory mechanisms in A. thaliana on a genomic scale. CressInt incorporates a variety of genome-wide data types relevant to gene regulation, including transcription factor (TF) binding site models, ChIP-seq, DNase-seq, eQTLs, and GWAS. Examples uses of CressInt are: (1) Identify TFs binding to the promoter of a gene of interest; (2) identify genetic variants that are likely to impact TF binding based on a ChIP-seq dataset; and (3) identify specific TFs whose binding might be impacted by phenotype-associated variants.

    The manuscript associated with CressInt was submitted for publication to Current Plant Biology in September 2015, and may be read online.

    A public web interface for CressInt is freely available at https://cressint.cchmc.org. Source code for the front-end web application (written in PHP) is available on Bitbucket.

  2. How should I cite CressInt?

    The manuscript associated with CressInt (X. Chen, et al., CressInt: A user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana, dx.doi.org/10.1016/j.cpb.2015.09.001) was published in the 15 September 2015 issue of Current Plant Biology.

    Citation information may be found here.

  3. What types of input will CressInt accept?

    CressInt accepts standard BED file input for genomic coordinates (described in more detail below) as well as coordinates of the form chr1:1-10,000,000, which you might want to copy-paste from the UCSC Genome browser.

    With the "Input type: Gene names" radio button selected, you may use the search box above the input field to find A. thaliana gene names from a comprehensive list (including aliases). You may also copy-and-paste a list of gene names directly into the input field, one per line. Letter case is not significant.

    In both cases, you also have the option of uploading a file containing the genomic coordinates or gene names. Both MS-DOS and Unix-style line endings are accepted.

    Work is in progress to add a FASTA input option.

  4. What is a BED file?

    The BED (or Browser Extensible Data) format describes a tab-delimited text file which contains information about the locations on chromosomes of regions of interest.

    The minimum recommended input for use with CressInt is BED4 format, comprised of the following fields:

    1. chrom – the name of the chromosome or scaffold (example: chr5, or scaffold10671)
    2. chromStart – the starting position of feature in the chromosome or scaffold
    3. chromEnd – the ending position of the feature in the chromosome or scaffold
    4. name – a name or reference ID for this coordinate (don't use spaces in this input field)

    Example: chr1 11873 14409 uc001aaa.3

    Currently, BED 3, BED 4, BED 5, or BED 6 file formats are supported in this version of CressInt (all designating the number of columns in the input). Missing columns will be supplied with placeholders, which is why you may see arbitrary seqXXX IDs applied to your input after submission, and in the intersection results.

    Strictly speaking, BED format requires that individual fields be delimited by "Tab" (\t) characters, but CressInt tries to be somewhat liberal and will generally accept any number of whitespace characters as a field delimiter. Don't use spaces within any of the optional fields (such as "name") to avoid problems processing your input.

    • A BED5 file has five attribute columns including score: chrom, start, end, name, and score.

      Example: chr1 11873 14409 uc001aaa.3 0

    • A BED6 file has six attribute columns including score and strand: chrom, start, end, name, score, and strand.

      Example: chr1 11873 14409 uc001aaa.3 0 +

  6. What is a Protein Binding Microarray?

    PBMs were originally developed by Martha Bulyk, and have since been adopted by many other groups. PBMs are unique because they offer an unbiased survey of the binding of a given protein. Briefly, PBMs contain ~40,000 double-stranded 60-base DNA probes, which are used to systematically measure the binding preferences to all possible DNA sequences – the probe sequences of a given PBM array are designed such that each of the 32,896 possible 8-base sequences appear in diverse flanking sequence contexts on 32 different probes. The resulting data, which track well with both in vivo-derived motifs and motifs derived from other in vitro assays, therefore offer a complete, robust, unbiased survey of the binding preferences of a given TF.

  7. What should the output of CressInt look like?

    Operation in "Intersect" mode (Mode 1) should produce just one results file: allresults.bed, which represents intersections of your provided gene coordinates with all available CressInt data sets.

    In "Find TF/SNPs" mode (Mode 2) and "Phenotypes to TF/SNPs" mode (Mode 3), you should get three results files: allresults.bed, PBMresults.bed, and SNPoutput.bed. Samples: Mode 2 and Mode 3.

    Other files incidental to the analysis may be offered for download, such as the list of input coordinates you initially provided or phenotype selections for Mode 3.

  8. What does "Mode 1" (or 2 or 3) mean?

    CressInt job results will refer to completed analysis as being one of three "modes." These correspond directly to the three radio buttons on the input form:

    • Mode 1 (Intersect): Just intersect input coordinates with selected datsets
    • Mode 2 (Find TF/SNPs): Identify SNPs within input coordinates, and the transcription factors whose binding they might affect.
    • Mode 3 (Phenotypes to TF/SNPs): Identify SNPs associated with phenotypes of interest, and the transcription factors whose binding they might affect.
  9. What does the "Unconstrain table" button do, exactly?

    The precise layout of tables in web pages is notoriously hard to control using just plain HTML. After analysis results are downloaded to your browser, a bit of JavaScript is used to compute optimal widths for all of the table columns, so that the entire table can be viewed within the "viewport" of your browser window. This, however, causes many cells' contents to be truncated, so a a small popup ("tooltip") over each cell will show you the untruncated value.

    Clicking the "Unconstrain table" button removes this constraint, allowing all table cells to go back to their original size. This will likely require that you use the horizontal scroll bars in order to see all the remaining columns which flow off into the right margin.

  10. How may I contact the developers?

    See something that needs improved? Let us know.

    You may contact Dr. Matthew Weirauch with questions or feedback at Matthew.Weirauch -at- cchmc.org. Please don't forget to change -at- to "@" before clicking "Send" in your email client.