Journal: International Journal of Molecular Sciences

Article Title: Differentially-Expressed Genes Associated with Faster Growth of the Pacific Abalone, Haliotis discus hannai

doi: 10.3390/ijms161126042

Figure Lengend Snippet: Growth traits of Pacific abalones used for RNAseq transcriptome analysis. The sizes of 80 abalone spats 200 days post-fertilization were measured. The values (mean ± standard deviation) represent those from 10 abalones selected from small, medium, and large sized individuals for RNAseq analysis.

Article Snippet: RNASeq and transcriptome analyses were carried out by Insilicogen Inc. (Suwon, Korea).

Techniques: Standard Deviation

Journal: Nucleic Acids Research

Article Title: LinkedOmics: analyzing multi-omics data within and across 32 cancer types

doi: 10.1093/nar/gkx1090

Figure Lengend Snippet: Functional impact of RB1 mutation on mRNA expression in Bladder Cancer. ( A ) In the TCGA BLCA (Bladder urothelial carcinoma) cohort, 1518 genes showed significant up-regulation (dark red dots, FDR < 0.01) in RB1 mutated samples whereas 1294 genes showed significant down-regulation (dark green dots, FDR < 0.01). ( B ) Among the most significant genes, up-regulation was found for CDKN2A and E2F1 (positive rank #1 and #22) whereas down-regulation was found for RB1 and CCND1 (negative rank #1 and #29). ( C ) The 1518 up-regulated genes were significantly enriched with transcriptional targets of E2F1 (Fisher's exact test, top 10 most enriched target sets).

Article Snippet: Genomic, epigenomic, and transcriptomic data for 32 TCGA cancer types were downloaded from the Firehose of the Broad Institute ( http://gdac.broadinstitute.org/ , January 2016 version).

Techniques: Functional Assay, Mutagenesis, Expressing

Journal: Nucleic Acids Research

Article Title: LinkedOmics: analyzing multi-omics data within and across 32 cancer types

doi: 10.1093/nar/gkx1090

Figure Lengend Snippet: Pan-cancer analysis for survival-associated gene expression signatures. ( A ) Twelve cancer types in the TCGA project with >100 death events. ( B ) The heat map shows the top 30 poor survival-associated genes. Each cell represents the signed –log 10 ( P -value). The right panel bar plot depicts corresponding meta-analysis based FDR. A and B share the same order of cancer types, as indicated below the heat map. ( C ) Increased expression of genes in the cell cycle pathway is associated with increased death risk (FDR<0.001, gene set enrichment analysis). Leading-edge genes are highlighted in red boxes in C. ( D–G ) Patients with above- (red) and below- (green) median APCDD1L mRNA abundance had significantly different survival rates in multiple cancer types such as bladder urothelial carcinoma (BLCA, D), head and neck squamous cell carcinoma (HNSC, E), kidney renal clear cell carcinoma (KIRC, F), and brain lower grade glioma (LGG, G).

Article Snippet: Genomic, epigenomic, and transcriptomic data for 32 TCGA cancer types were downloaded from the Firehose of the Broad Institute ( http://gdac.broadinstitute.org/ , January 2016 version).

Techniques: Gene Expression, Expressing

Journal: Horticulture Research

Article Title: Role of female-predominant MYB39-bHLH13 complex in sexually dimorphic accumulation of taxol in Taxus media

doi: 10.1093/hr/uhac062

Figure Lengend Snippet: Integrated metabolomic and transcriptomic analyses for the taxol pathway. a Diagram of the taxol biosynthesis pathway. b Expression analysis of genes encoding enzymes related to the paclitaxel biosynthesis pathway between female and male T. media trees. The color scale ranges from −2 to +2 on a log 2 scale. c Differential accumulation of several metabolites related to the taxol pathway between female and male T. media trees. The color scale ranges from −1 to +1 on a log 2 scale.

Article Snippet: We are also grateful to LC Sciences (Hangzhou, China) for metabolomic and transcriptomic analyses.

Techniques: Expressing

Journal: BMC Evolutionary Biology

Article Title: Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

doi: 10.1186/s12862-018-1302-2

Figure Lengend Snippet: Subtree for Aquatic clade, color-coded by organismal classification. Asterisks indicate lower confidence sequences from organisms with transcriptome-only support, when these occur within sparsely or weakly represented phyla. These include Euphausia superba and Meganyctiphanes norvegica as representatives of the class Malacostraca, respectively, within the sparsely represented phylum Arthropoda; as well as the two representatives from the phylum Mollusca . Taxon names include genus and species labels (e.g. Rota_ta for Rotaria tardigrada ) as well as specific protein or nucleotide database identifiers

Article Snippet: Within the Aquatic group, several sequences putatively belonging to Oreochromis niloticus (a fish commonly known as tilapia) proved to be identical to confirmed genome and transcriptome sequences from Amoebidium parasiticum , a microorganism that is not found in association with tilapia but which had been sequenced at the same institute (Broad Institute).

Techniques:

Journal: BMC Evolutionary Biology

Article Title: Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

doi: 10.1186/s12862-018-1302-2

Figure Lengend Snippet: Partial eukaryotic organism tree showing widespread losses of ST-like and/or Aquatic GDPD-like SMaseD/PLD genes, according to a model of ancient duplication followed by vertical descent. Colors indicate nodes and branches retaining both paralogs (purple), ST-like only (red), Aquatic only (blue), or neither (black). Branch labels indicate important clades: M, Metazoa; C, Cnidaria; D, Deuterostomia; P, Protostomia; S, Spiralia; E, Ecdysozoa; A, Arthropoda; H, Hexapoda (see Materials and Methods). Each taxon (phylum or class in most cases) is annotated with the number of genomes containing a PLD gene, divided by the total number of NCBI representative genomes assembled at scaffold level or higher (May 2018). Taxa marked with * also include additional genomes in which PLD genes were detected in unassembled (or assembled but not NCBI-deposited) genomic data. Taxa marked with ^ showed no PLD genes in NCBI representative genomes but did have hits in transcriptomes from multiple genera. Taxa marked with ~ showed one or several hits but with contamination suspected. This tree topology and evolutionary model imply 15 losses of ST-like and 18 losses of Aquatic genes, and additional losses would be necessary to explain incomplete conservation within certain taxa. While such extensive loss seems unlikely, the insets (dashed boxes) show distributions within Anthozoa and Rotifera that are consistent with at least three ST-like or Aquatic gene loss events in these phyla alone. The Anthozoan tree includes genera with transcriptome data only (italicized). The presence of scattered proteobacterial homologs in the Aquatic clade supports a role for lateral gene transfer in contributing to the observed sparse species distribution

Article Snippet: Within the Aquatic group, several sequences putatively belonging to Oreochromis niloticus (a fish commonly known as tilapia) proved to be identical to confirmed genome and transcriptome sequences from Amoebidium parasiticum , a microorganism that is not found in association with tilapia but which had been sequenced at the same institute (Broad Institute).

Techniques:

Journal: Scientific Reports

Article Title: Aging and putative frailty biomarkers are altered by spaceflight

doi: 10.1038/s41598-024-57948-5

Figure Lengend Snippet: Genelab datasets analyzed in the manuscript.

Article Snippet: OSD-99 , Rodent Research-1 (RR1) NASA Validation Flight: Mouse extensor digitorum longus muscle transcriptomic and epigenomic data , Galazka J, Globus R "Rodent Research 1", GeneLab, Version 4, http://doi.org/10.26030/1h3m-3q49 , Extensor digitorum longus muscle.

Techniques: Gene Expression, Expressing, Biomarker Discovery, Irradiation