IPA Winter Release 2014

Go beyond pathway analysis and deeper into your RNA-Seq data with the IPA Winter Release 2014. In this release, human isoforms from Ensembl are now available alongside human isoforms from RefSeq on the IPA Isoform View.

With IPA’s enhanced support for human RNA-Seq data, scientists are now able to quickly identify differentially expressed isoforms between condition and control samples, and interpret the impact of expression changes in the context of biological processes, disease and cellular phenotypes, and molecular interactions.

Enhanced RNA-Seq support includes human Ensembl-based isoforms

Take advantage of both sources on Gene Views, by toggling between RefSeq and Ensembl to visualize associated isoforms on the Isoform View. In addition, understand which isoforms from your dataset are most significantly differentially expressed for additional follow-up.

Figure 1: Ensembl isoform view for the gene DRAP1. Ensembl has annotated nine isoforms (splice variants) for this human gene, the first five of which are protein-coding. Two RNA-seq datasets are overlaid onto this view revealing that in one dataset, three isoforms are up-regulated, while in the other dataset one isoform is down-regulated.

Find the significant isoforms in your RNA-seq data with new human isoform visualizations

Quickly identify which genes in your human RNA-seq dataset have expression data for one or more isoforms. On networks and pathways, nodes with multiple isoforms in your dataset are surrounded with a yellow glow. This helps you quickly identify significant differentially expressed genes that may have splicing patterns of interest. Double click a node of interest to see which isoforms are differentially expressed in your dataset

Figure 2:  Isoform indicators on a network. The yellow glow around certain nodes indicates the genes that have expression values for more than one isoform in your dataset. For example ACTB, VIM, PKM, and IGF2 are glowing in the screenshot above, whereas EGR1 is not.

Figure 2: Isoform indicators on a network. The yellow glow around certain nodes indicates the genes that have expression values for more than one isoform in your dataset. For example ACTB, VIM, PKM, and IGF2 are glowing in the screenshot above, whereas EGR1 is not.

Figure 3:  Isoform data in Molecule Summary. Double clicking on a node that has a glow shows a preview of the isoform-level data in the Molecule Summary window. The differential expression is represented as small rectangles, one per isoform. IGF2 has eight isoforms annotated by Ensembl, two of which have expression data in this dataset (they are upregulated as indicated with red filled rectangles). One isoform’s expression is chosen by IPA to represent the ortholog—it is indicated with the checkmark.

Figure 3: Isoform data in Molecule Summary. Double clicking on a node that has a glow shows a preview of the isoform-level data in the Molecule Summary window. The differential expression is represented as small rectangles, one per isoform. IGF2 has eight isoforms annotated by Ensembl, two of which have expression data in this dataset (they are upregulated as indicated with red filled rectangles). One isoform’s expression is chosen by IPA to represent the ortholog—it is indicated with the checkmark.

Figure 4:  Isoform data on Gene View. Clicking in the Molecule Summary (see Figure 3) will show the Gene View with isoform-level expression data from the dataset shown at the right next to its corresponding isoform. In this example dataset, two of the shorter protein isoforms are significantly expressed.

Figure 4: Isoform View. Clicking in the Molecule Summary (see Figure 3) will show the Gene View with isoform-level expression data from the dataset shown at the right next to its corresponding isoform. In this example dataset, two of the shorter protein isoforms are significantly expressed.

Quickly identify significant connections with new layout options for networks

You can change the default layout of networks and My Pathways using the new Layout Options which emphasize different aspects of the network depending on which layout you select: Organic, Circular, Radial, Hierarchical or Subcellular giving you more versatility than ever before for how you look at your data.

A particular network visualized with each of the five layout options. Each layout emphasizes different aspects of the network. Note that the hierarchical and radial layout options behave differently if a subset of the nodes is selected before choosing that option.

A particular network visualized with each of the five layout options. Each layout emphasizes different aspects of the network. Note that the hierarchical and radial layout options behave differently if a subset of the nodes is selected before choosing that option.

Figure 5: A particular network visualized with each of the five layout options. Each layout emphasizes different aspects of the network. Note that the hierarchical and radial layout options behave differently if a subset of the nodes is selected before choosing that option.