Scalable, interactive and hierarchical visualization of virus taxonomic data

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Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors - Fig 2

<p><b>A</b>) Left Panel: variants obtained from exome sequencing of tumor samples from Her2-enriched Breast Cancer (HER2+ BRC) patients. Right Panel: Variants identified as potential drivers. <b>B)</b> Left Panel: variants obtained from exome sequencing of tumor samples from ER positive Breast Cancer (ER+ BRC) patients. Right Panel: Variants identified as potential drivers. Color codes are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194790#pone.0194790.g001" target="_blank">Fig 1</a>.</p

Left Panel: variants obtained from exome sequencing of tumor samples from Triple Negative Breast Cancer (TNBC) patients.

<p>Genes were grouped based on relevant biological activities/pathways. Right Panel: Variants identified as potential drivers (red: high-confidence drivers; gold: lower confidence drivers. Inset: Color coding scheme for types of mutations (mis-sense, termination, splice site, in-frame deletion), confidence of driver likelihood (high-confidence, lower confidence). Asterisks indicate mutations present in the COSMIC (<u>C</u>atalogue <u>o</u>f <u>S</u>omatic <u>M</u>utations in <u>C</u>ancer) database. The same coding scheme is used in Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194790#pone.0194790.g002" target="_blank">2</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194790#pone.0194790.g005" target="_blank">5</a>.</p

Absolute numbers of previously described and putative drivers identified in this study in different tumor types.

<p>Inset: color coding reflecting tumor types. Abbreviations: TNBC (Triple Negative Breast Cancer), HER2+BC (Her2-enriched Breast Cancers), ER+BC (ER-positive Breast Cancer), CRC (Colorectal Cancer), LUAD (Lung Adenocarcinoma), LUSC (Lung Squamous Cell Carcinoma), SCC (Squamous Cell Carcinoma), SRC (Soft Tissue Sarcoma), NET (Neuroendocrine Tumor), TC (Thymic Carcinoma), GC (Gastric Cancer), SIGRCA/KRUK (Signet Ring Adenocarcinoma/Krukenberg Cell Tumor), CUPO (Carcinoma of Unknown Primary Origin).</p

Previously described and putative drivers identified in this study grouped by functional classes or biological pathways.

<p>Pathway or functional class assignment was based on Gene Ontology supplemented by individual PathCards searches (<a href="http://pathcards.genecards.org/" target="_blank">http://pathcards.genecards.org/</a>) for each gene. Inset: color coding reflecting tumor types. Abbreviations: TNBC (Triple Negative Breast Cancer), HER2+BC (Her2-enriched Breast Cancers), ER+BC (ER-positive Breast Cancer), CRC (Colorectal Cancer), LUAD (Lung Adenocarcinoma), LUSC (Lung Squamous Cell Carcinoma), SCC (Squamous Cell Carcinoma), SRC (Soft Tissue Sarcoma), NET (Neuroendocrine Tumor), TC (Thymic Carcinoma), GC (Gastric Cancer), SIGRCA/KRUK (Signet Ring Adenocarcinoma/Krukenberg Cell Tumor), CUPO (Carcinoma of Unknown Primary Origin).</p

Left Panel: variants obtained from exome sequencing of tumor samples from Colorectal Cancer (CRC) patients.

<p>Right Panel: Variants identified as potential drivers. Color codes are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194790#pone.0194790.g001" target="_blank">Fig 1</a>.</p

Additional file 4: Table S4. of Comparative genome analysis of Mycoplasma pneumoniae

Variants in ORF6 excluding the large variation region (nucleotides 186572-187144), relative to the M129 reference strain. (XLSX 11 kb

Additional file 1: Table S1. of Comparative genome analysis of Mycoplasma pneumoniae

Initial assembly characteristics. (XLSX 19 kb

Additional file 1: of Age and fecal microbial strain-specific differences in patients with spondyloarthritis

Code for processing of 16S sequences with DADA2 and for shotgun sequence analysis with HUMAnN2. (DOCX 12 kb

Additional file 3: of Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile

Relative abundance of microbes at family level taxonomy. (XLSX 69 kb