IsoSeq data updated

• Brain/Liver/Merged IsoSeq Tracks showing IsoSeq Read alignments to rn7.
• Created IsoSeq UCSC Genome Browser track hub
• Fixed a gene display bug in the genome browser
• Downloads Added(RNA-Seq Downloads):
• IsoSeq samples high quality Isoform FASTQ files.
• Rn7.2 merged genome alignment of FASTQ files
• Rn7.2 merged transcriptome as GTF

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HRDP v7 UCSC Genome Browser track hubs are available now. Downloads -> UCSC.

• Tissue specific transcriptomes and merged transcriptomes
• Tissue/strain specific read count tracks both total(sum of 3 replicates) or sampled( randomly sampled reads to match the strain with the fewest reads)
• Merged across strain read counts and then sampled to represent 5 Billion reads.
• Splice junctions from merged and 5 billion read sampled Bam files.

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• HRDP v6 TPM Data available via REST API and Downloads
• HRDP v7 TPM Data available via REST API and Downloads
• Added TPM and Heritablility summaries to gene reports.
• Bug Fixes

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• Sampled counts from every strain are now available as well as total counts.
• You can create a custom view and select total/sampled count and choos the density of the count tracks.
• Bug Fixes

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• You can now create gene lists from Genome Browser tables - Filter tables from tracks, eQTLs, WGCNA based on expression/tissue and then use gene list tools on the list.
• Implemented a reasonable region restriction of 5Mbp for now. - We are working to create a less detailed view that will be displayed in larger regions.
• Bug Fixes

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• Version 3.7.3 has been released with the following updates.
  • RNA-Seq eQTLs based on HRDP
  • Heritability based on HRDP
  • TPM summary
  • Track Table filtering
  • Table export to clipboard, csv, xls, and PDF
  • Ensembl and Reconstruction based eQTLs/TPM/Heritability

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• Version 3.7.2 has been released with the following updates.
  • RNA-Seq eQTLs
    • Gene Track Summaries now include RNA-Seq based eQTL summaries
    • Modules for a region can be selected base on overlap of the module QTL with the region.
    • Genes with an eQTL that overlaps the region are now available based on RNA-Seq and Microarrays
  • Custom Views
    • Total Counts for all 45 strains to date are available.
  • Read counts for all 45 strains are available to add as browser tracks.
  • Bug Fixes

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• Version 3.7.1 has been released with the following updates.
  • Downloads
    • Tissue Specific/Merged Reconstruction GTFs
    • Normalized Expression Values for Ensembl/Reconstruction, Gene/Transcript, Strain Means/Individual values
  • Custom Views
    • Build a custom view on the fly by selecting a few check boxes simply select sissue and track types.
    • Views can be named and saved for future use

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• Version 3.7 has been released with HRDP v5.
  • Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains now including the F344/Stm and LE/Stm strains.
  • Updated WGCNA, expression values, eQTLs, and transcriptomes are available.
  • Transcript level expression is available for the full panel.
  • Transcript level eQTLs are now available once you've selected a gene.
  • Transcript level WGCNA is coming in the next 1-2 months.
• CircularRNA data is availble now. This includes predictions from BNLx/SHR in Brain/Heart/Liver using CIRI 2.0 and CircExplorer2. Also Heart left ventricle includes data from more than 12,000 previously described cirRNAs using cirRNA arrays. Full reports are coming soon but the browser includes tracks with annotation and structure all available data.

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• HRDP v4 Data is available
  • Transcriptomes are now based on the full HXB/BXH RI panel in brain and liver and available inbred strains except for the F344/Stm and LE/Stm. The FXLE/LEXF parents will be included in HRDP v5.
  • Updated WGCNA, expression values, eQTLs, and transcriptomes are available.
  • Transcript level expression is available again now for the full panel.
  • Transcript level WGCNA is coming in the next 1-2 months.
• New gene list circos plot eQTL image/browser.
• Genome Browser Section shortcuts
• Links to Gene Relationship Literature Search, Gene and Addiction Literature Searches, GeneNetwor SNP Browser

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• Beta Testing cloud version now
• Most of the changes occurred behind the scenes and users will not see much of a difference with 2 exceptions.
  • The domain is now going to be phenogen.org.
  • Microarray analysis will not be available in this version. You should still have access to previously uploaded arrays and any analysis performed.
• The major changes should provide better reliability and performance while reducing maintenance time to allow for development of new tools. Write us and let us know what you would find useful.
• New Features and data are coming soon so keep checking back on the new site.

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• Inbred Read Depth Tracks
  • Added Read Depth Tracks in Brain and Liver for the new inbred strains: ACI, Dark-Agouti, Cop, F344-NCl, F344-NHsd, LEW-Crl, LEW-SsNHsd, SHRSP, SR-JrHsd, SS-JrHsd, and WKY

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• PhenoGen IDs
  • The Genome/Transcriptome Data Browser can now look up genes by either their gene or transcript PhenoGen ID.
  • Updated External Database IDs

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• Recombinant Inbred Small RNA
  • Expression - The expression tab now will summarize small RNA-Seq expression for the RI panel in both Whole Brain and Liver. There is both a heatmap and scatter plot available to display the values.

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• Recombinant Inbred Total RNA
  • Expression - The expression tab now will summarize RNA-Seq expression and heritability for the RI panel in both Whole Brain and Liver. There is both a heatmap and scatter plot available to display the values.
  • WGCNA - New WGCNA data is available based on RNA-Seq reconstructed transcripts in Whole Brain and Liver.
    
    • You now have the option to view RNA-Seq or Array based WGCNA modules.
    • Meta modules have be generated to allow browsing related modules.

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• Small RNA Rat small RNA tracks from Brain, Heart, Liver based on the small RNA-Seq. Including counts from the parental strains. Tracks include known and novel small RNAs. Novel RNA's were predicted by MiRDeep and SNOSeeker.
• Merged Total RNA Transcriptome Added a track with the merged transcriptome from the 3 available tissues and assigned new unique PhenoGen IDs to all novel transcripts.

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• Rn6 All four tissues of the HXB Mircoarray datasets are available with Rn6 versions. The genome browser will now let you select either Rn5 or Rn6. Gene list tools that depend on the genome version now allow selection of Rn5 or Rn6 based on the version that you want.
• WGCNA Heart and Liver modules are now available based on the Rn6 version of the data. Whole Brain has an updated version using Rn6.
• Site wide search You can now use google on the site to search on PhenoGen.
• Repeat Mask Track in the Genome Browser We've made the UCSC repeat mask data available as a track in the browser.

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• Anonymous Gene Lists You now can bring in a Gene List and use our tools without a login. You should remember that we are storing a unique id in your browser so you can return to your list on subsequent visits. If you loose this the only way to recover the gene lists linked to that ID is by email recovery. This only works if you link your email. If you don't link an email there is potential that you will loose access to your list/analysis.

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• Security Enhancements The biggest change that you will see is that we've redirected you to https://phenogen.ucdenver.edu . Please update your bookmarks as we're now requiring use of HTTPS. This will encrypt all of the data sent between you and our server.
  
  We're hoping to be able to offer new features such as registering and/or signing in using a Google account or allowing users to store data on Google Drive. Our next major update will include microarrays and RNA-Seq all updated to Rn6, although in the browser both Rn5 and Rn6 will be available.

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• Gene Lists
  • Updated tab format - the new format allows you to submit a new analysis, view previous results, and see the current status of running analyses.
  • Gene Ontology Summaries - summaries similar to the WGCNA module summaries can now be run on a Gene List.
  • MultiMiR - MultiMiR supports rat miRNAs now so you can view miRNAs predicted and validated to target a gene.
• Genome/Transcriptome Data Browser
  • MultiMiR - you can now view a summary for selected Rat genes.

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• New Weighted Gene Co-expression Network Analysis(WGCNA) Views.
  • Gene Ontology View:
    • View an interactive expandable sunburst plot of each GO Domain(Biological Process, Molecular Function, and Cellular Component). Provides a summary of all the GO terms assigned to genes in the module.
    • View graphic form and CSV exportable table form. Both are interactive and can be used to explore the GO term tree.
  • miRNA targeting (multiMiR) View:
    • View/Filter miRNAs that target genes in the module. Visualize targets of miRNAs and the correlation between genes targeted. Filter to look at specific miRNAs or miRNAs targeting specific genes.
    • View graphic form and CSV exportable table form.
• Rat Transcriptomes Updated Brain, Liver, and Heart(New)
  • Strain Specific Transcripts - Now transcripts specific to a strain are color coded to quickly visualize splicing differences between strains.
  • Updated Brian and Liver Transcriptome - New versions of the brain and liver transcriptome are available.
  • Added Heart Transcriptome - We've added the first version of the heart transcriptome.
  • Transcriptome Versioning - Missing a transcript of interest in the new transcriptome? You can view previous version of the transcriptome now by selecting a previous version in the track settings.

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• Weighted Gene Co-expression Network Analysis(WGCNA) Results.
  • Available for both Mouse and Rat Brain.
  • Module View:
    • Transcripts both Ensembl Annotated and RNA-Seq reconstructed
    • Transcripts connectedness showing positive and negative correlation of transcript expression.
    • View graphic form and CSV exportable table form.
  • eQTL Module View:
    • View CIRCOS plot:
      • Genome with regions below the selected P-value cutoff highlighted.
      • Customizable with include/exclude chromosomes and adjust P-value cutoff.
      • View graphic form and CSV exportable table form.
    • CSV exportable table form with SNP name/location and P-value.
• Where to find WGCNA Data
  • Genome/Transcriptome Data Browser - Modules can be viewed for all genes in a region of interest or for a single gene.
  • Gene Lists - Modules can be viewed for all genes in the gene list along with a summary of modules containing the most genes from the list.

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• Genome/Transcriptome Data Browser
  • Views have been completely updated to allow us to offer multiple views that change based on the species viewed, and now you can build your own view.
    • Easily view different types of data in the same region by switching between views with only 3 clicks.
    • Build your own view by from a blank view or copy a view and modify it. You can control the included tracks, track settings, and track order.
    • Bring in your own data and include custom tracks in views. Now supporting Bed, BedGraph, BigBed, and BigWig files.
    • Save views/tracks to the server for portability.(See below for more information)
  • Updated Data:
    • Mouse Brain RNA-Seq - We've added a transcriptome reconstruction, splice junctions, and stranded RNA-Seq read depth tracks for the parental strains of the LXS panel(ILS/ISS).
    • Rat Heart RNA-Seq - Splice juctions, stranded RNA-Seq read depth tracks are available now for the parental strains of the HXB/BXH panel(BN-Lx/SHR). The transcriptome reconstruction will be available later.
    • Rat Brain/Liver RNA-Seq -Updated splice juctions and stranded(Liver) or polyA+/total(Brain) RNA-Seq read depth tracks are available now. Updated transcriptome reconstructions will be available later.
  • New custom track file support:
    • bedGraph - uploaded 20MB size limit
    • bigBed - remotely hosted, no size limit
    • bigWig - remotely hosted, no size limit
    • bed - we still support bed files, uploaded, 20MB size limit
  • Custom View/Tracks will save to the server if you login to the site before creating them. If you have logged into the site any views or tracks will save to the server so you can view them on any device that you login from and can reduce the risk of loosing them.
  • Don't want to register or login, don't worry everything will still work, custom tracks and views are saved locally via one of two mechanisms, either local storage or cookies in older browsers. If you clear these you will loose your custom views or tracks.

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• Genome/Transcriptome Data Browser
  • Rearranged Ensembl and Rat Brain Transcriptome Reconstruction Tracks into a seperate track for each source.
    • Brain transcripts were removed from Ensembl tracks and added to their own track to mirror the additional tissue tracks to be added in the next few months.
    • Region summary tables now include Liver transcripts
  • Improved the feature selection
    • Changed how sections are displayed and now hide the region section completely when a feature is selected
    • Now the selected area is highlighted in the top graphic.
  • Improved navigation by adding a back button to step back through zooming and panning allowing better control than just resetting to the original region when the page loaded.
  • Improved tool tip images for RNA-Seq read depth count tracks- the image will now refresh with higher resolution count data if you pause for a fraction of a second.

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• Gene List Analysis
  • Incorporated multiMiR(an R package available here) to summarize validated and predicted targets of miRNA from 14 databases.
    • After selecting a mouse Gene List (support for Rat will be available in the future), you will see a new miRNA Targeting Gene(multiMiR) tab.
    • You may run a new analysis
    • Select a previous analysis:
      • View:
        • a small table sumarizing the number of validated/predicted genes targeted.
        • a larger table with further detail about all the validated/predicted genes and databases.
      • Select an miRNA to view details:
        • view a list of all predicted database hits and scores
        • view a list of all validated database hits with experiment details and pubmed reference
    • Future additions:
      • run multiMiR with disease/drug targeting
      • in the browser run multiMiR on genes or miRNA in a region of interest

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• Genome/Transcriptome Data Browser:
  • Incorporated multiMiR(an R package available here) to summarize validated and predicted targets of miRNA from 14 databases.
    • To use start with a mouse gene (rat will be available in the future) in the Genome/Transcriptome Browser. You will see a new miRNA Targeting Gene(multiMiR) tab.
    • View a list of validated and predicted miRNAs targeting the selected gene.
    • Select a miRNA:
      • view a list of all predicted database hits and scores
      • view a list of all validated database hits with experiment details and pubmed reference
      • view a list of all genes targeted by that miRNA
    • Future additions:
      • run multiMiR on a Gene List
      • run multiMiR on genes or miRNA in a region of interest
      • run multiMiR with disease/drug targeting
  • Try it out

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• Genome/Transcriptome Data Browser:
  • Liver RNA-Seq Data
    • Added Liver RNA-Seq transcriptome reconstruction track (BN-Lx only for now - SHR will be added soon)
    • Added Liver RNA-Seq splice junction track (BN-Lx only for now - SHR will be added soon)
    • Added Liver RNA-Seq stranded read depth count track (BN-Lx only for now - SHR will be added soon)
  • PolyA sites
    • A new track indicating polyadenylation sites. For now only known sites are included, but soon predicted sites will be included.
  • Other changes since v2.10:
    • Previews of many features in the information windows that open when you hover over a feature.
    • Saving an browser image directly to your computer is now possible look for the icon.
    • Improved navigation. This tool bar
      
      now allows you to control the default mouse function when you click making it easier to move along the genome, zoom by selecting a region, and reorder tracks without moving left or right.
    • Support for small custom tracks. You may upload small <20MB custom track files and display them along with changing the display type and coloring.
    • Added Rat/Mouse RefSeq tracks.
    • The browser adjusts to the size of the window. Before you were limited to 1000pixel width, now it will redraw to fit any width window including spanning monitors.
    • Transcripts from Ensembl/RefSeq now indicate any annotated untranslated region.
    • Detailed probe set view had a bug on Mac OS X, now that is fixed in the Oracle runtime environment. If you update Java this bug will be corrected.
    • In large regions transcripts are grouped into genes. In smaller regions transcripts are drawn separately, but the user can force drawing transcripts if desired.
    • View genome sequence and 3 possible amino acid sequences when zoomed in below 3000bp.
  • Try it out          View Demonstration

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• New Mouse Genome: Our public data has been updated to Mm10. Probes were aligned to the mouse genome version 10 and then new masks were generated. The Public LXS data uses a strain specific mask with only Parental ILS and ISS SNPs included. All of three versions of the dataset were renormalized to use the new masks. Previous results are still available, but new analyses will use the new versions of the dataset.


• Detailed Transcription Information renamed to Genome/Transcriptome Data Browser
  • The page is now centered around a new D3/SVG graphic that makes the page more like a genome browser:
    • The graphics are interactive    
    You can easily zoom and move along the genome to browse features. You can select a feature to pull up a detailed another detailed interactive image of that feature or a report summarizing the data available for the feature.
    • Three different customizable views   
    You can view Genomic Features
    
    You can view Transcriptome Features
    You can view a combination of both types of features.
    With all views the tracks displayed are saved so you can move around the genome viewing with the same view or you can flip between two or three views looking at different tracks.
  • The Gene and Region views have been unified to provide a similar interface whether you enter a gene or browse a region.
  • New Demos:
    • A new short demonstration of navigating using the Genome/Transcriptome Data Browser
    • A new version of the previous demonstration showing how to use the Genome/Trascriptome Data Browser to look at regions of interest
  • Try it out          View Demonstration

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• New Rat Genome: All of our public data has been updated to Rn5. Probes were aligned to the rat genome version 5 and then new masks were generated. All of the datasets were renormalized to use the new masks. Previous results are still available, but new analyses will use the new versions of the datasets.


• Detailed Transcription Information:
  • Regions have been updated to include more RNA-Seq data(Rat only):
    • UCSC Image allows control of individual tracks    
    The image now allows you to turn tracks off and on individually as well as gives you control of the density of the track.
    • Several New Image Tracks(Rat only)   
    There are new tracks available for the Rat:
    • Small RNAs from Brain RNA-Seq.
    • Long Non-Coding RNAs from Brain RNA-Seq
    • SNP/Indels- from DNA Sequencing of the BN-Lx and SHR strains.
    • Helicos Read Counts - Read Counts from the Helicos Brain RNA-Seq
    • Features located in region table includes additional information    
    The table includes the following changes:
    1. IDs used in the image are listed in the table
    2. Columns were added to allow the user to sort the table based on tracks in the image.
    3. Rows in the table are color coded to match the track in the image.
    4. SNP/indel counts within an exon for each gene (rat only) were added.
    5. Small RNA information such as read sequence and total read counts were added (rat only).
    6. Links have been added for NCBI, UniProt, RGD, MGI, and Allen Brain Atlas for each gene listed in the table.
  • Gene views have been updated to include the following:
    • The list of features in a region is now displayed for the region of a gene.    
    All features within the genomic region of the gene will be listed in the table. This includes long non-coding RNAs and small RNA.
    • UCSC Image allows control of individual tracks    
    The image now allows you to turn tracks off and on individually as well as gives you control of the density of the track.
    • New Several Image Tracks(Rat only)   
    There are new tracks available for the Rat:
    • Small RNAs from Brain RNA-Seq.
    • Long Non-Coding RNAs from Brain RNA-Seq
    • SNP/Indels- from DNA Sequencing of the BN-Lx and SHR strains.
    • Helicos Read Counts - Read Counts from the Helicos Brain RNA-Seq
    • eQTLs for a gene are displayed on the same page   
    Instead of opening in a seperate page you can now navigate between features found in the gene region, eQTLs and Detailed Affy Probeset information using tabs on the page.
  • Try it out


• Rat Parental Strian DNA Sequence Available: DNA sequence information from parental strain (BN-Lx and SHR) of the HXB/BXH recombinant inbred panel is available: The strain-specific genome of parental strains of the Public Rat Array/RNA-Seq datasets is available for download and the SNPs/indels can be displayed in the image on the Detailed Transcriptome Information page. View in downloads

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• Detailed Transcription Information:
  • Now you can view regions too(instead of entering a gene symbol, enter a region chr1:1-50,000)
    • View UCSC Image of region    
    The image shows genes in the region and bQTLs. Optionally you may view additional information such as Ensembl transcripts and RNA-Seq transcripts(Rat only), UCSC/Affymetrix exon expression data, and homologus human chromosome regions and proteins.
    • For Rat RNA-Seq transcripts from Brain are included
    RNA-Seq data(Available in the downloads section) was used to create a reconstructed transcriptome. Those transcripts can be displayed and the number of transcripts found can be compared to the Ensembl transcript annotations. When viewing Detailed Transcription Information at the gene level more information is available.
    • View Heritability and Detection Above Background across tissues availble for genes in the region   
    We have exon array data for 2 recombinant inbred panels and various tissues (ILSXISS Mice(Whole Brain) and HXB/BXH Rats(Whole Brain, Heart, Liver, Brown Adipose). This data is summarized for each region to include the # and avgerage heritability of probesets with a significant heritability and # and average percentage of samples where probesets were detected above background. These are summarized for each gene in each tissue.
    • View eQTLs for genes in the region   
    For genes in the region eQTL with the minimum P-value and its location is summarized across tissues. All locations and tissues can be summarized in a circos plot.
    • View bQTLs overlapping the region   
    All public bQTLs from MGI and RGD with a defined location that overlaps the current region are displayed in summary table that also links to the associated databases.
    • View genes controlled from the region   
    eQTLs are calculated for the recombinant inbred panels at the Gene level(Affy Exon Transcript Clusters having a core annotation)). This is used to return a list of genes that have a core transcript cluster and an eQTL that overlaps the region.
  • Translate a region of interest from Human/Mouse/Rat to Mouse/Rat to view PhenoGen data.
  • Try it out


• Demos: View the video demo of our Detailed Transcription Information features, with more demos coming soon. View Demo


• MEME Updated to v4.9: MEME v4.9 is now available. Old results are still avialable, but new analysis will use 4.9 which will also have better graphics display and will link to the main meme server for further analysis. Available in Gene List Analysis


• Human Genotyping Data Available: Affymetrix Genome-Wide Human SNP Array 6.0 data for alcohol dependent subjects receiving outpatient treatment at the Medical University of Vienna (Austria). View in downloads

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• Detailed Transcription Information:
  • View Parental Strain Differential Expression
  • View Parental Strain(Rat) Transcriptome Reconstruction
  • View Panel Heritability/Detection Above Background accross tissues
  • View Panel Expression accross tissues
  • View Exon Correlation Tool
  • Identify exons within a gene that are not expressed
  • Identify exons within a gene with low heritability
  • Use correlation patterns among exons to identify expressed isoforms.
  • View eQTL information
• New Menu Navigation: The new Menu system allows users to easily get between functions that previously required clicking through multiple pages.
• Download Resources without Logging in: Resources that used to require a login are now available without logging in.

• Exon level analysis tools:Analyze probeset-level data for the public exon arrays.
• Exon-exon correlation heatmaps: Perform exon-exon correlation within a gene:
  1. Select a gene (from a gene list or enter your own). and
  2. Select an exon dataset (from Rats or Mice).
  3. Select Brain(Mouse or Rat), Heart(Rat), Liver(Rat), or Brown Adipose tissues(Rat).
  4. View any Ensembl transcript for the gene, or compare two transcripts side by side.
• Download RNA-sequencing:SAM files from three replicates of polyA+ RNA from whole brain of two rat strains and three replicates of total RNA from whole brain of the same two rat strains can now be downloaded in the Download Resources tab.
• Data storage format:A new system for storing data in the database and HDF5 files speeds up normalization, filtering, and statistics. This is currently implemented to support analysis on Affymetrix Exon arrays, but future updates will implement the new storage methods for the remaining array types.

Informatics Workshop Overview:


Example WGCNA miRNA targeting View:

Example WGCNA Gene Ontology View:

Example WGCNA Module View:

Example WGCNA eQTL Module View:

Example Region View:

Example Tissue View showing Array and RNA-Seq Data and a zoomed in view from holding the mouse over a region: