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Fasting Project - Analysis Results
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This section provides the identifiers and notations used to report the analysis results on this website.
It also provides a description of some parts of the analysis and some comments that may help understand the results.

Experimental Design

  • List of Tissues
  • List of Conditions
  • List of Groups
  • List of Time Points
  • List of Technical Groups
  • List of Replicates

Gene Expression Analysis

  1. exons and junctions for each gene are first extracted by taking the union of the exons and junctions of all the known isoforms of the gene in the RefSeq database.
  2. the resulting exonic positions are then filtered to remove any position overlapped by an exon of a distinct gene.
  3. genes with at least one exon left after filtering were considered viable for the standard RNA-seq analysis ORIG and were included in the ORIG-GENES dataset.
  4. the ORIG-GENES dataset contains 23,989 gene entries and includes several genes repeated on the genome on different chromosomes. The dataset is made available for download and visualization in the Annotations tab of this website.
  5. the corresponding set of exonic positions is noted ORIG-EXONS on the website.
  1. exons and junctions for each gene are first extracted by taking the intersection of the exons and junctions of all the known isoforms of the gene in the RefSeq database. Introns are extracted following the same protocol.
  2. the resulting exonic and intronic positions are then filtered to remove any position overlapped by any exonic or intronic position of a distinct gene.
  3. genes reported several times on the genome at different locations were removed.
  4. genes with at least one exon and one intron larger than the sequencing reads (100 bp) left after filtering were considered viable for the EISA expression analysis and were included in the EISA-GENES dataset.
  5. the EISA-GENES dataset contains 19,433 gene entries and does not include any gene repeated on the genome. The dataset is made available for download and visualization in the Annotations tab of this website.
  6. the corresponding sets of exonic and intronic positions are respectively noted EISA-EXONS and EISA-INTRONS on the website.
  • List of Expression Analyses

    The two expression analyses aim to estimate gene expression levels using either exonic reads or intronic reads. A major difference between the two analyses is the set of gene annotations used to estimate the gene expression levels. The ORIG expression analysis was performed based on the gene annotations noted ORIG-GENES (see below) containing a fairly large number of genes while the EISA expression analysis was performed based on the gene annotations noted EISA-GENES (see below) containing less genes (genes with no introns were removed for instance) and using different exon coordinates for many of the genes present in the ORIG-GENES annotations. Standard RNA-seq analyses implement an as much as possible strategy where aligned reads will be counted for a given gene as long as at least one gene isoform reports the corresponding positions as exonic. Only exons from distinct genes with overlapping positions are discarded to remove the corresponding ambiguities. At the opposite, the EISA expression analysis requires a different approach where aligned reads are counted for a given gene only if all known isoforms of the gene report the corresponding positions as exonic (or intronic). Positions reported both exonic and intronic depending on the gene isoform are discarded from the analysis to remove the corresponding ambiguities. The EISA-GENES annotations therefore contain not only less genes but also less exonic positions than the ORIG-GENES annotations.

  • List of Gene Annotations

    The gene annotations used during the ORIG and EISA analyses contain many genes for which no expression was observed for all 72 replicates in the experiment. Also, due to a very low coverage of the introme, many genes ended up to be covered in the best case by a very low number of sequencing reads, too low to distinguish between expression and DNA contamination. Expression results extracted for all the genes present in the gene annotations described above were thus filtered to remove any gene for which there is nothing to expect from any downstream analysis either because the gene is not expressed in any replicate or because the coverage is dramatically low for all the replicates and does not allow any reliable further analysis of the gene. Results available on the website are provided for these filtered gene lists only.

This section provides general statistics on the sequencing data (quantity of reads and PHRED quality scores) for each replicate included in the group selected above or for each technical group in the experiment when the All Groups option is selected above. In the second case, the 3 replicates in each technical group are combined together and are treated as a single replicate.

This section provides detailed mapping statistics for each replicate included in the group selected above or for each technical group in the experiment when the All Groups option is selected above. In the second case, the 3 replicates in each technical group are combined together and are treated as a single replicate. Additional comments for each figure are provided below.

  • Figure #1: percentage of reads uniquely located on the reference genome, on the exome, and on the introme.
  • Figure #2: corresponding mean coverage values for the exome and for the introme.
  • Figure #3: percentage of genes covered by at least one exonic or intronic read.

This section provides the gene annotations used to perform the gene expression analyses.
Both datasets are available (1) for download via the links provided below and (2) for visualization via the table located on the bottom of this page.

Direct Download

  • TSV File Format:
  • XLS File Format:

Data Visualization