Gao et al.Page 26
NIH-PA Author ManuscriptNIH-PA Author ManuscriptNIH-PA Author ManuscriptSci Signal. Author manuscript; available in PMC 2014 September 10.
Fig. 5. The Mutations tab
To generate these results, the query was limited to mutations for ERBB2 in the indicatedcancer study. Four of the 10 ERBB2 mutations in colorectal cancer occur in a hotspot in thekinase domain. (A) The graphical view shows the Pfam protein domains and the positions ofspecific mutations. The length of the line connecting the mutation annotation to the proteinis indicative of the number of samples that have the mutation. The most recurrent mutationsare labeled in the graphical view. (B) The tabular view provides additional informationabout all mutations in each query gene.
Gao et al.Page 27
NIH-PA Author ManuscriptNIH-PA Author ManuscriptNIH-PA Author ManuscriptSci Signal. Author manuscript; available in PMC 2014 September 10.
Fig. 6. The Protein Changes tab
When available in the cancer study selected, results related to protein or phosphoproteinabundance are provided through this tab. In this example, glioblastoma (GBM) samples withalterations in PTEN have increased phosphorylated AKT. (A) Phosphoproteins with
different amounts when comparing PTEN-altered samples and PTEN-wild-type samples.The list is sorted by P values from a two-sample t-test. (B) Boxplot representation of therelative amount of AKT pT308 in PTEN-altered and PTEN-wild-type samples. This plot isgenerated by clicking the icon in the Plot column of the tabulated data.
Gao et al.Page 28
NIH-PA Author ManuscriptFig. 7. The Survival tab
The example shows the overall survival (A) and the disease-free survival (B) of ovariancancer patients with or without BRCA1 or BRCA2 mutations. The red curves in the Kaplan-Meier plots includes all tumors with a BRCA1 or BRCA2 germline or somatic mutation, theblue curves includes all samples without a BRCA1 or BRCA2 mutation.
NIH-PA Author ManuscriptNIH-PA Author ManuscriptSci Signal. Author manuscript; available in PMC 2014 September 10.
Gao et al.Page 29
NIH-PA Author ManuscriptNIH-PA Author ManuscriptNIH-PA Author ManuscriptFig. 8. The Network tab
The example shows network analysis of EGFR networks in serous ovarian cancer. (A)
Network view of the EGFR and ERBB2 neighborhood in serous ovarian cancer (TCGA dataset) rendered with Cytoscape Web (34).The query genes, EGFR and ERBB2, are outlinedwith a thick border, and nearest neighbor genes are color-coded by their alteration frequencyin ovarian cancer. One can display drugs that target EGFR or ERBB2 (hexagons; orangeindicates FDA-approved), as well as details about genomic alterations and links to externalresources for any gene in the network (bottom left, example MYC). (B) The “Gene Legend”accessed from the “Legend” button. Mousing over any gene in the network or single-clicking the gene displays multidimensional genomic data (copy number, mutation, andmRNA expression) onto all nodes in the network. (C) The “Interaction Legend” accessedfrom the “Legend” button. Double-clicking the edge displays additional details about theinteraction between the two nodes. Edges can represent different interaction types (color-coded, such as “reacts with”). (D) Options for filtering, cropping, and searching the networkare shown.
Sci Signal. Author manuscript; available in PMC 2014 September 10.
Gao et al.NIH-PA Author ManuscriptNIH-PA Author ManuscriptNIH-PA Author ManuscriptPage 30
Fig. 9. Cross-cancer queries
(A) Users initiate a query against all cancer studies in three steps. (B) The results aredisplayed as a histogram of the alteration frequencies of the query gene (or genes) acrosscancer studies. The example shows that TP53 mutation frequencies are the highest insquamous cell carcinomas of ovary, lung, and head and neck.
Sci Signal. Author manuscript; available in PMC 2014 September 10.