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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.
More information about supported input formats and general usage can be found on the Help and FAQs page. See the associated manuscript and the "Case Study" buttons below for specific examples. The associated manuscript, submitted to Current Plant Biology in September 2015, may be read online.
Intersect Find TF/SNPs Phenotypes to TF/SNPs
Genomic coordinates Gene names FASTA sequence(s)
0W 0W_GH_FT 0W_GH_LN 2W 4W 8W 8W_GH_FT 8W_GH_LN After_Vern_Growth Anthocyanin_10 Anthocyanin_16 Anthocyanin_22 Aphid_number As As_CFU2 As2 As2_CFU2 As75 At1 At1_CFU2 At2 At2_CFU2 avrB avrPphB avrRpm1 avrRpt2 B11 Bacterial_titer Bs Bs_CFU2 Ca43 Cd114 Chlorosis_10 Chlorosis_16 Chlorosis_22 Co59 Cu65 DSDS50 DW Emco5 Emoy* Emwa1 Fe56 FLC FRI FT_Diameter_Field FT_Duration_GH FT_Field FT_GH FT10 FT16 FT22 FW Germ_10 Germ_16 Germ_22 Germ_in_dark Hiks1 Hypocotyl_length K39 LC_Duration_GH LD LDV Leaf_roll_10 Leaf_roll_16 Leaf_roll_22 Leaf_serr_10 Leaf_serr_16 Leaf_serr_22 LES LFS_GH Li7 LN10 LN16 LN22 LY Mg25 Mn55 Mo98 MT_GH Na23 Ni60 Noco2 P31 Rosette_Erect_22 RP_GH S34 SD SDV Se82 Secondary_Dormancy Seed_bank_133-91 Seed_Dormancy Seedling_Growth Silique_16 Silique_22 Storage_28_days Storage_56_days Storage_7_days Trichome_avg_C Trichome_avg_JA Vern_Growth Width_10 Width_16 Width_22 YEL Zn66
Choose phenotypes to identify associated SNPs, and the transcription factors whose binding they might affect.
Selecting a phenotype from the list at the left will show an extended description here.
Lines refer to genomic data sets from distinct experiments or tissue types. "Any" refers to a data sets with no tie to a specific experiment, phenotype, or tissue type (e.g., the GWAS data set or SNP list)
/ (default: -1000 / +0 relative to gene body)
alphanumerics and _.+-@:?!() are allowed
Submitting job to cluster...