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Dev Biol
2017 Jun 15;4262:155-164. doi: 10.1016/j.ydbio.2016.02.034.
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XenMine: A genomic interaction tool for the Xenopus community.
Reid CD
,
Karra K
,
Chang J
,
Piskol R
,
Li Q
,
Li JB
,
Cherry JM
,
Baker JC
.
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The Xenopus community has embraced recent advances in sequencing technology, resulting in the accumulation of numerous RNA-Seq and ChIP-Seq datasets. However, easily accessing and comparing datasets generated by multiple laboratories is challenging. Thus, we have created a central space to view, search and analyze data, providing essential information on gene expression changes and regulatory elements present in the genome. XenMine (www.xenmine.org) is a user-friendly website containing published genomic datasets from both Xenopus tropicalis and Xenopus laevis. We have established an analysis pipeline where all published datasets are uniformly processed with the latest genome releases. Information from these datasets can be extracted and compared using an array of pre-built or custom templates. With these search tools, users can easily extract sequences for all putative regulatory domains surrounding a gene of interest, identify the expression values of a gene of interest over developmental time, and analyze lists of genes for gene ontology terms and publications. Additionally, XenMine hosts an in-house genome browser that allows users to visualize all available ChIP-Seq data, extract specifically marked sequences, and aid in identifying important regulatory elements within the genome. Altogether, XenMine is an excellent tool for visualizing, accessing and querying analyzed datasets rapidly and efficiently.
Fig. 1. An illustration of the XenMine homepage. (A) Enter a gene name to access the Gene page report. (B) Enter a list of genes to determine GO and publication enrichments. (C) Click to input, save, view and compare lists, or to be taken directly to JBrowse. (D) Popular Template queries can be found here and under the Templates button at the top of the page.
Fig. 2. Analysis of ChIP-Seq datasets. (A) ChIP-Seq peak tracks at the lefty locus visualized in JBrowse that indicate the presence of a putative enhancer. The red box outlines a regioncentered at the gene of interest, containing peaks for histone marks H3K4Me1, H3K27Ac and the transcription factor Smad2/3. (B) By selecting a region of interest, users can download track data from the reference sequence (Ref Seq) track by clicking on the arrow next to the RefSeq track and selecting Save Track Data, highlighted in the red box. (C) Track data is downloaded in FASTA format for further analysis. (D) Transcription factor and histone mark peaks are annotated on the Gene Page Reports. The link for each peak gives detailed information about this genomic region, including the source of the data, the peak height and score and any overlapping features within the peak.
Fig. 3. Sorting and filtering data to obtain biological information. A) The search template Retrieve RNA-Seq expression scores for a given gene retrieves a table with 117 rows showing the expression of dazl in all experiments available on XenMine. (B) The distribution of expression values can be displayed in graph form, allowing the user to choose the desired range of expression values; in this case, from 50 to 186 (red box). (C) The Expression Scores column can be sorted in descending order by clicking the arrow button, highlighted in the red box. (D) The data can be downloaded in multiple formats or exported to Galaxy or GenomeSpace by clicking on the Export button found at the top of the results table (highlighted in the red box in A).
Fig. 4. Comparisons of datasets. (A) Under Lists on the XenMine homepage, users can manually enter or upload a list of genes for analysis. (B) XenMine automatically returns details of the genes, including genomic coordinates, along with GO Enrichment Publication Enrichment. (C) Lists saved in MyMine can be compared using the Union, Intersect, Subtract, or Asymmetric Difference tools.
Fig. 5. Manipulating the results table for desired output. (A) From the template Retrieve binding sites that overlap a specific gene, we find the called ChIP-Seq peaks near the gsc gene. By clicking on Manage Columns, outlined in the red box, we add the data of interest, in this case RNA-Seq expression data (see Supp. Fig. 3). (B) The added columns can be seen in the resulting table, highlighted in the red box. (C) Filtering the highlighted columns for Stage 9 results in the ChIP-Seq peaks associated with the gsc gene when it is expressed.
