Using The Cancer Genome Atlas as an Inquiry Tool in the Undergraduate Classroom.


:Undergraduate students in the biomedical sciences are often interested in future health-focused careers. This presents opportunities for instructors in genetics, molecular biology, and cancer biology to capture their attention using lab experiences built around clinically relevant data. As biomedical science in general becomes increasingly dependent on high-throughput data, well-established scientific databases such as The Cancer Genome Atlas (TCGA) have become publicly available tools for medically relevant inquiry. The best feature of this database is that it bridges the molecular features of cancer to human clinical outcomes-allowing students to see a direct connection between the molecular sciences and their future professions. We have developed and tested a learning module that leverages the power of TCGA datasets to engage students to use the data to generate and test hypotheses and to apply statistical tests to evaluate significance.


Front Genet


Frontiers in genetics


Hankey W,Zanghi N,Crow MM,Dow WH,Kratz A,Robinson AM,Robinson MR,Segarra VA




Has Abstract


2020-12-16 00:00:00








  • Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation.

    abstract::In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interacti...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Sunnucks P,Morales HE,Lamb AM,Pavlova A,Greening C

    更新日期:2017-03-03 00:00:00

  • Could magnetic resonance provide in vivo histology?

    abstract::THE DIAGNOSIS OF A SUSPECTED TUMOR LESION FACES TWO BASIC PROBLEMS: detection and identification of the specific type of tumor. Radiological techniques are commonly used for the detection and localization of solid tumors. Prerequisite is a high intrinsic or enhanced contrast between normal and neoplastic tissue. Ident...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Dominietto M,Rudin M

    更新日期:2014-01-13 00:00:00

  • Construction and Analysis of a ceRNA Network Reveals Potential Prognostic Markers in Colorectal Cancer.

    abstract::Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide and is derived from an accumulation of genetic and epigenetic changes. This study explored potential prognostic markers in CRC via the construction and in-depth analysis of a competing endogenous RNA (ceRNA) network, which was gene...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Guo L,Yang G,Kang Y,Li S,Duan R,Shen L,Jiang W,Qian B,Yin Z,Liang T

    更新日期:2020-05-08 00:00:00

  • Genetic Model to Study the Co-Morbid Phenotypes of Increased Alcohol Intake and Prior Stress-Induced Enhanced Fear Memory.

    abstract::Posttraumatic Stress Disorder (PTSD) is a complex illness, frequently co-morbid with depression, caused by both genetics, and the environment. Alcohol Use Disorder (AUD), which also co-occurs with depression, is often co-morbid with PTSD. To date, very few genes have been identified for PTSD and even less for PTSD com...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Lim PH,Shi G,Wang T,Jenz ST,Mulligan MK,Redei EE,Chen H

    更新日期:2018-11-27 00:00:00

  • Programmable Base Editing of the Sheep Genome Revealed No Genome-Wide Off-Target Mutations.

    abstract::Since its emergence, CRISPR/Cas9-mediated base editors (BEs) with cytosine deaminase activity have been used to precisely and efficiently introduce single-base mutations in genomes, including those of human cells, mice, and crop species. Most production traits in livestock are induced by point mutations, and genome ed...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Zhou S,Cai B,He C,Wang Y,Ding Q,Liu J,Liu Y,Ding Y,Zhao X,Li G,Li C,Yu H,Kou Q,Niu W,Petersen B,Sonstegard T,Ma B,Chen Y,Wang X

    更新日期:2019-03-15 00:00:00

  • Emerging applications of read profiles towards the functional annotation of the genome.

    abstract::Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data is typically a resul...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Pundhir S,Poirazi P,Gorodkin J

    更新日期:2015-05-19 00:00:00

  • Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53.

    abstract::Chemicals, toxicants, and environmental stressors mediate their biologic effect through specific modes of action (MOAs). These encompass key molecular events that lead to changes in the expression of genes within regulatory pathways. Elucidating shared biologic processes and overlapping gene networks will help to bett...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Funderburk KM,Auerbach SS,Bushel PR

    更新日期:2017-10-24 00:00:00

  • The Effect of Dopamine Antagonist Treatment on Auditory Verbal Hallucinations in Healthy Individuals Is Clearly Influenced by COMT Genotype and Accompanied by Corresponding Brain Structural and Functional Alterations: An Artificially Controlled Pilot Stud

    abstract::Few studies have been conducted to explore the influence of the catechol-o-methyltransferase (COMT) genotype on the severity of and treatment efficacy on auditory verbal hallucination (AVH) symptoms in healthy individuals with AVHs (Hi-AVHs). We hypothesized that the efficacy of dopamine antagonist treatment on AVHs i...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Zhuo C,Xu Y,Zhang L,Jing R,Zhou C

    更新日期:2019-03-06 00:00:00

  • A new method for estimating the demographic history from DNA sequences: an importance sampling approach.

    abstract::The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main differenc...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Ait Kaci Azzou S,Larribe F,Froda S

    更新日期:2015-08-07 00:00:00

  • Analysis of Single Nucleotide Variants in CRISPR-Cas9 Edited Zebrafish Exomes Shows No Evidence of Off-Target Inflation.

    abstract::Therapeutic applications of CRISPR-Cas9 gene editing have spurred innovation in Cas9 enzyme engineering and single guide RNA (sgRNA) design algorithms to minimize potential off-target events. While recent work in rodents outlines favorable conditions for specific editing and uses a trio design (mother, father, offspri...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Mooney MR,Davis EE,Katsanis N

    更新日期:2019-10-11 00:00:00

  • Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution.

    abstract::Recently, an increasing number of studies sequence multiple biopsies of primary tumors, and even paired metastatic tumors to understand heterogeneity and the evolutionary trajectory of cancer progression. Although several algorithms are available to infer the phylogeny, most tools rely on accurate measurements of muta...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Wu P,Hou L,Zhang Y,Zhang L

    更新日期:2020-02-07 00:00:00

  • The SNP rs13147758 in the HHIP Gene Is Associated With COPD Susceptibility, Serum, and Sputum Protein Levels in Smokers.

    abstract:Background:Genetic association studies have identified single nucleotide polymorphisms (SNPs) related to chronic obstructive pulmonary disease (COPD) susceptibility. The aim of this study was to identify HHIP genetic variants associated with COPD, pulmonary function, and serum and sputum HHIP protein levels in Mexican ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Ortega-Martínez A,Pérez-Rubio G,Ambrocio-Ortiz E,Nava-Quiroz KJ,Hernández-Zenteno RJ,Abarca-Rojano E,Rodríguez-Llamazares S,Hernández-Pérez A,García-Gómez L,Ramírez-Venegas A,Falfán-Valencia R

    更新日期:2020-09-24 00:00:00

  • Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis.

    abstract::Hepatocellular carcinoma (HCC) remains hard to diagnose early and cure due to a lack of accurate biomarkers and effective treatments. Hence, it is necessary to explore the tumorigenesis and tumor progression of HCC to discover new biomarkers for clinical treatment. We performed weighted gene co-expression network anal...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Gu Y,Li J,Guo D,Chen B,Liu P,Xiao Y,Yang K,Liu Z,Liu Q

    更新日期:2020-02-28 00:00:00

  • Long noncoding RNAs: a potential novel class of cancer biomarkers.

    abstract::Long noncoding RNAs (lncRNAs) are a novel class of RNA molecules defined as transcripts longer than 200 nucleotides that lack protein coding potential. They constitute a major, but still poorly characterized part of human transcriptome, however, evidence is growing that they are important regulatory molecules involved...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Yarmishyn AA,Kurochkin IV

    更新日期:2015-04-23 00:00:00

  • Bias, accuracy, and impact of indirect genetic effects in infectious diseases.

    abstract::Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not followi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Lipschutz-Powell D,Woolliams JA,Bijma P,Pong-Wong R,Bermingham ML,Doeschl-Wilson AB

    更新日期:2012-10-22 00:00:00

  • QTL Mapping for Agronomic and Adaptive Traits Confirmed Pleiotropic Effect of mog Gene in Black Gram [Vigna mungo (L.) Hepper].

    abstract::Organ size and architecture of plants are important traits affecting crop yield and agronomic practices. An induced mutant, multiple-organ gigantism (MOG), of black gram (Vigna mungo) has been obtained, which shows gigantic leaves, fruit, seed, and architecture (plant height) but lower number of pods per plant. These ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Somta P,Chen J,Yimram T,Yundaeng C,Yuan X,Tomooka N,Chen X

    更新日期:2020-06-30 00:00:00

  • Redundancy of the genetic code enables translational pausing.

    abstract::The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptiv...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: D'Onofrio DJ,Abel DL

    更新日期:2014-05-20 00:00:00

  • Transcription factor binding at enhancers: shaping a genomic regulatory landscape in flux.

    abstract::The mammalian genome is packed tightly in the nucleus of the cell. This packing is primarily facilitated by histone proteins and results in an ordered organization of the genome in chromosome territories that can be roughly divided in heterochromatic and euchromatic domains. On top of this organization several distinc...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Palstra RJ,Grosveld F

    更新日期:2012-09-28 00:00:00

  • Neurologic Manifestations as Initial Clinical Presentation of Familial Hemophagocytic Lymphohistiocytosis Type2 Due to PRF1 Mutation in Chinese Pediatric Patients.

    abstract::Familial hemophagocytic lymphohistiocytosis Type 2 (FHL2) associated central nervous system (CNS) involvement is less understood in children, especially when considering neurologic manifestations as part of the initial presentation. We conducted a retrospective review of the clinical manifestations and genetic abnorma...

    journal_title:Frontiers in genetics



    authors: Feng WX,Yang XY,Li JW,Gong S,Wu Y,Zhang WH,Han TL,Zhuo XW,Ding CH,Fang F

    更新日期:2020-03-04 00:00:00

  • Comprehensive Analysis of Respiratory Burst Oxidase Homologs (Rboh) Gene Family and Function of GbRboh5/18 on Verticillium Wilt Resistance in Gossypium barbadense.

    abstract::Respiratory burst oxidase homologs (Rbohs) play a predominant role in reactive oxygen species (ROS) production, which is crucial in plant growth, differentiation, as well as their responses to biotic and abiotic stresses. To date, however, there is little knowledge about the function of cotton Rboh genes. Here, we ide...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Chang Y,Li B,Shi Q,Geng R,Geng S,Liu J,Zhang Y,Cai Y

    更新日期:2020-09-11 00:00:00

  • Exploring genome-wide - dietary heme iron intake interactions and the risk of type 2 diabetes.

    abstract:AIMS/HYPOTHESIS:Genome-wide association studies have identified over 50 new genetic loci for type 2 diabetes (T2D). Several studies conclude that higher dietary heme iron intake increases the risk of T2D. Therefore we assessed whether the relation between genetic loci and T2D is modified by dietary heme iron intake. M...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Pasquale LR,Loomis SJ,Aschard H,Kang JH,Cornelis MC,Qi L,Kraft P,Hu FB

    更新日期:2013-01-30 00:00:00

  • Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.).

    abstract::Plant basic helix-loop-helix (bHLH) transcription factors are involved in the regulation of various biological processes in plant growth, development, and stress response. However, members of this important transcription factor family have not been systematically identified and analyzed in pepper (Capsicum annuum L.)....

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Zhang Z,Chen J,Liang C,Liu F,Hou X,Zou X

    更新日期:2020-09-25 00:00:00

  • Proband Whole-Exome Sequencing Identified Genes Responsible for Autosomal Recessive Non-Syndromic Hearing Loss in 33 Chinese Nuclear Families.

    abstract::Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous disease involving more than 70 pathogenic genes. However, most ARNSHL families have small-sized pedigrees with limited genetic information, rendering challenges for the molecular diagnosis of these patients. Therefore, we attempted to es...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Sang S,Ling J,Liu X,Mei L,Cai X,Li T,Li W,Li M,Wen J,Liu X,Liu J,Liu Y,Chen H,He C,Feng Y

    更新日期:2019-07-17 00:00:00

  • The Trp73 Mutant Mice: A Ciliopathy Model That Uncouples Ciliogenesis From Planar Cell Polarity.

    abstract::p73 transcription factor belongs to one of the most important gene families in vertebrate biology, the p53-family. Trp73 gene, like the other family members, generates multiple isoforms named TA and DNp73, with different and, sometimes, antagonist functions. Although p73 shares many biological functions with p53, it a...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Marques MM,Villoch-Fernandez J,Maeso-Alonso L,Fuertes-Alvarez S,Marin MC

    更新日期:2019-03-15 00:00:00

  • MiR-486-5p Serves as a Good Biomarker in Nonsmall Cell Lung Cancer and Suppresses Cell Growth With the Involvement of a Target PIK3R1.

    abstract::MicroRNAs are a class of noncoding RNAs that can be involved in the regulation of gene expression in cancers, including lung cancer. Our previous research has shown that miR-486-5p is one of the most downregulated microRNAs in tissue and serum samples of lung cancer as a good diagnostic biomarker. The objective of thi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Tian F,Wang J,Ouyang T,Lu N,Lu J,Shen Y,Bai Y,Xie X,Ge Q

    更新日期:2019-07-26 00:00:00

  • Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cells.

    abstract::The comet assay is a simple and cost effective technique, commonly used to analyze and quantify DNA damage in individual cells. The versatility of the comet assay allows introduction of various modifications to the basic technique. The difference in the methylation sensitivity of the isoschizomeric restriction enzymes...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Lewies A,Van Dyk E,Wentzel JF,Pretorius PJ

    更新日期:2014-07-07 00:00:00

  • Missense Mutations of Human Hsp60: A Computational Analysis to Unveil Their Pathological Significance.

    abstract::Two chaperonopathies have been linked to mutations in the human hsp60 (hHsp60; HSPD1) gene, but other existing variants might cause diseases, even if there is no comprehensive information about this possibility. To fill this vacuum, which might be at the basis of misdiagnoses or simply ignorance of chaperonopathies in...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Vitale AM,Conway de Macario E,Alessandro R,Cappello F,Macario AJL,Marino Gammazza A

    更新日期:2020-08-18 00:00:00

  • Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria.

    abstract::Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, includ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Alcorta J,Alarcón-Schumacher T,Salgado O,Díez B

    更新日期:2020-11-05 00:00:00

  • TMEM205 Is an Independent Prognostic Factor and Is Associated With Immune Cell Infiltrates in Hepatocellular Carcinoma.

    abstract::Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide despite the availability of diverse treatment strategies. Much research progress has been made regarding immunotherapy but the effects remain unsatisfactory, highlighting the urgent need for novel immune-related therapy target...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Rao J,Wu X,Zhou X,Deng R,Ma Y

    更新日期:2020-10-14 00:00:00

  • Aberrant epigenetic regulators control expansion of human CD34+ hematopoietic stem/progenitor cells.

    abstract::Transcription is a tightly regulated process ensuring the proper expression of numerous genes regulating all aspects of cellular behavior. Transcription factors regulate multiple genes including other transcription factors that together control a highly complex gene network. The transcriptional machinery can be "hijac...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Faridi F,Ponnusamy K,Quagliano-Lo Coco I,Chen-Wichmann L,Grez M,Henschler R,Wichmann C

    更新日期:2013-11-28 00:00:00