If genomic position is not inputed, processed nuclear receptor data of the whole selected chromosome would be returned. The result page would include five options for each dataset:
"Download: WIG" to download the wiggle file with variable step for ChIP_chip datasets and fixed 30bp space for ChIP_seq datasets; the ChIP_chip wiggle file is converted from bar file
using MAT group's unpublished bar2wig.py script.
"View: WIG" to view the wiggle file on UCSC genome browser; the file is displayed in vertical bars rather than default colored blocks; users could view additional information such as refseq genes by selecting
certain customerized options in UCSC genome browser.
"Download: BED" to download the peak files in bed format with a 1e-5 pvalue cut-off.
"View: BED" to view the bed file in UCSC genome browser.
"Download:XLS" to download peak files in xls format with a 1e-5 pvalue cut-off; the xls files have additional information such as FDR values and peak summit positions, which are not included in the bed files.
It is worth noting that for users' conveniences, all the above files are named by combined information of species, cell type, factor, condition, lab and chromosome number. For example, a bed file with the name
"Human_MCF-7_ESR1_E2-45min_Brown_chr5.bed" includes the peaks in chromosome five of human ESR1 dataset generated by Dr. Brown's lab in MCF-7 cell line after 45 minutes treatment of estrogen.
If co-regulators is selected, the result page would return transcription factor and PolII datasets in the chosen cell type. If epigenome option is selected, the result page would return the histone modification
and nucleasome positioning datasets in the chosen cell type. If transcriptome option is selected, the result page would return the expression indexes and differential FDRs of genes in the matched condition as the nuclear
receptor datasets. If motif option is selected, the result page would return HRE and co-regulator motif hit positions, each with a likelihood score for users to select their own cuts. If targets option is selected, the result page would return the predicted direct targets of the selected nuclear receptor in the selected cell type, each target gene being annotated with a simulated FDR value.
If the genomic position is inputed, the result page would return files in the same formats as mentioned above, except that the files are not of the whole chromosome, but within the inputed chromosome range.
To view all the ChIP
peak and motif hit files at the same time in UCSC genome browser, users could just click on "Go to UCSC genome browser" option at the top of the page.
Please pay attention that to limit the searching time to serveral seconds, we exclude the wiggle files in the returned page of selected chromosome range.