Data Viz

Modified

February 1, 2025

A selection of data visualizations I generated from genomics/multi-omics and clinical datasets generated using ggplot2, ComplexHeatmap, plotly R, and Gviz among others. Most figures presented here are found in published journal articles for projects I supported.


Unsupervised clustering figures including unsupervised hierarchical clustering, Non-metric multidimensional scaling (NMDS), and Uniform Manifold Approximation and Projection (UMAP)


Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

Bertrums et al. (2023)

CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR t cell target

Le et al. (2022)

CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes

Huang et al. (2021)

CEBPA bZip mutations are associated with favorable prognosis in de novo AML: A report from the childrens oncology group

Tarlock et al. (2021)

The clinical and biological characteristics of NUP98-KDM5A in pediatric acute myeloid leukemia

Noort et al. (2020)

Consensus machine learning for gene target selection in pediatric AML risk

Smith (2019)

Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: A retrospective study by the i-BFM study group

Noort et al. (2018)

Heatmaps illustrating effect size for changes in gene expression or enrichment of GO terms/pathway analysis. Genomic rearrangments representations include lollipop plots, circos, and oncoprints.


ETS family transcription factor fusions in childhood AML: Distinct expression networks and clinical implications

Smith et al. (2021)

Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

Bertrums et al. (2023)

Pathologic, cytogenetic, and molecular features of acute myeloid leukemia with megakaryocytic differentiation: A report from the childrens oncology group

Chisholm et al. (2023)

Genome-wide gene expression profiles throughout human malaria parasite liver stage development

Kappe et al. (2023)

Comprehensive transcriptome profiling of cryptic CBFA2T3GLIS2 fusionpositive AML defines novel therapeutic options: A COG and TARGET pediatric AML study

Smith et al. (2019)

Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia

Bertrums et al. (2023)

CEBPA bZip mutations are associated with favorable prognosis in de novo AML: A report from the childrens oncology group

Tarlock et al. (2021)

Comprehensive transcriptome profiling of cryptic CBFA2T3GLIS2 fusionpositive AML defines novel therapeutic options: A COG and TARGET pediatric AML study

Smith et al. (2019)

Time-to-event analysis, including overall survival and event-free survival, and generated Kaplan-Meier curves.


Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia

Huang et al. (2022)

Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia

Huang et al. (2022)

Long noncoding RNA expression independently predicts outcome in pediatric acute myeloid leukemia

Farrar et al. (2023)

Illustration of effect size and significance with volcano plots. Longitudinal relationships are shown by lineplot with error represented as ribbon plots. Dot plots represent covariate relationships between mRNAs and miRNAs, and can be used to represent many other types of relationships with two categorigal variables. Dot plots are also useful for representing the level of enrichment (dot size and fill color) for GO terms/pathway analysis when x-axis is a numeric p-value.


Comprehensive transcriptome profiling of cryptic CBFA2T3GLIS2 fusionpositive AML defines novel therapeutic options: A COG and TARGET pediatric AML study

Smith et al. (2019)

Genome-wide gene expression profiles throughout human malaria parasite liver stage development

Kappe et al. (2023)

Distribution plots, such as boxplots, violin plots, histograms and ridge plots/density plots, are used to visualize the distribution of sample data, including gene expression values, fluorescence values, patient scores, etc.


Comprehensive transcriptome profiling of cryptic CBFA2T3GLIS2 fusionpositive AML defines novel therapeutic options: A COG and TARGET pediatric AML study

Smith et al. (2019)

Long noncoding RNA expression independently predicts outcome in pediatric acute myeloid leukemia

Farrar et al. (2023)

Long noncoding RNA expression independently predicts outcome in pediatric acute myeloid leukemia

Farrar et al. (2023)

References

The majority of figures presented here are found in published journal articles, referenced here. The publications page lists additional articles for projects I supported.

Bertrums, E. J. M., Smith, J. L., Harmon, L., Ries, R. E., Wang, Y.-C. J., Alonzo, T. A., Menssen, A. J., Chisholm, K. M., Leonti, A. R., Tarlock, K., Ostronoff, F., Pogosova-Agadjanyan, E. L., Kaspers, G. J. L., Hasle, H., Dworzak, M., Walter, C., Muhlegger, N., Morerio, C., Pardo, L., … Meshinchi, S. (2023). Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica. https://doi.org/10.3324/haematol.2022.281653
Chisholm, K. M., Smith, J., Heerema-McKenney, A. E., Choi, J. K., Ries, R. E., Hirsch, B. A., Raimondi, S. C., Wang, Y.-C., Dang, A., Alonzo, T. A., Sung, L., Aplenc, R., Gamis, A. S., Meshinchi, S., & Kahwash, S. B. (2023). Pathologic, cytogenetic, and molecular features of acute myeloid leukemia with megakaryocytic differentiation: A report from the childrens oncology group. Pediatric Blood & Cancer. https://doi.org/10.1002/pbc.30251
Farrar, J. E., Smith, J. L., Othus, M., Huang, B. J., Wang, Y.-C., Ries, R., Hylkema, T., Pogosova-Agadjanyan, E. L., Challa, S., Leonti, A., Shaw, T. I., Triche, T. J., Gamis, A. S., Aplenc, R., Kolb, E. A., Ma, X., Stirewalt, D. L., Alonzo, T. A., & Meshinchi, S. (2023). Long noncoding RNA expression independently predicts outcome in pediatric acute myeloid leukemia. Journal of Clinical Oncology, 41(16), 2949–2962. https://doi.org/10.1200/jco.22.01114
Huang, B. J., Smith, J. L., Farrar, J. E., Wang, Y.-C., Umeda, M., Ries, R. E., Leonti, A. R., Crowgey, E., Furlan, S. N., Tarlock, K., Armendariz, M., Liu, Y., Shaw, T. I., Wei, L., Gerbing, R. B., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2022). Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33244-6
Huang, B. J., Smith, J. L., Wang, Y.-C., Taghizadeh, K., Leonti, A. R., Ries, R. E., Liu, Y., Kolekar, P., Tarlock, K., Gerbing, R., Crowgey, E., Furlan, S. N., Shaw, T. I., Hagiwara, K., Wei, L., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2021). CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Advances, 5(23), 4963–4968. https://doi.org/10.1182/bloodadvances.2021004965
Kappe, S., Zanghi, G., Patel, H., Camargo, N., Smith, J., Bae, Y., Hesping, E., Boddey, J., Flannery, E., Chuenchob, V., Fishbaugher, M., Mikolajczak, S., Roobsoong, W., Sattabongkot, J., Hayes, K., & Vaughan, A. (2023). Genome-wide gene expression profiles throughout human malaria parasite liver stage development. https://doi.org/10.21203/rs.3.rs-3689897/v1
Le, Q., Hadland, B., Smith, J. L., Leonti, A., Huang, B. J., Ries, R., Hylkema, T. A., Castro, S., Tang, T. T., McKay, C. N., Perkins, L., Pardo, L., Sarthy, J., Beckman, A. K., Williams, R., Idemmili, R., Furlan, S., Ishida, T., Call, L., … Meshinchi, S. (2022). CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR t cell target. Journal of Clinical Investigation, 132(22). https://doi.org/10.1172/jci157101
Noort, S., Wander, P., Alonzo, T. A., Smith, J., Ries, R. E., Gerbing, R. B., Dolman, M. E. M., Locatelli, F., Reinhardt, D., Baruchel, A., Stary, J., Molenaar, J. J., Stam, R. W., Heuvel-Eibrink, M. M. van den, Zwaan, C. M., & Meshinchi, S. (2020). The clinical and biological characteristics of NUP98-KDM5A in pediatric acute myeloid leukemia. Haematologica, haematol.2019.236745. https://doi.org/10.3324/haematol.2019.236745
Noort, S., Zimmermann, M., Reinhardt, D., Cuccuini, W., Pigazzi, M., Smith, J., Ries, R. E., Alonzo, T. A., Hirsch, B., Tomizawa, D., Locatelli, F., Gruber, T. A., Raimondi, S., Sonneveld, E., Cheuk, D. K., Dworzak, M., Stary, J., Abrahamsson, J., Arad-Cohen, N., … Zwaan, C. M. (2018). Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: A retrospective study by the i-BFM study group. Blood, 132(15), 1584–1592. https://doi.org/10.1182/blood-2018-05-849059
Smith, J. L. (2019). Consensus machine learning for gene target selection in pediatric AML risk. In biorxiv.
Smith, J. L., Ries, R. E., Farrar, J. E., Alonzo, T. A., Gerbing, R. B., Leonti, A. R., Hylkema, T. A., Gamis, A. S., Aplenc, R., Kolb, E. A., Nguyen, C., Meerzaman, D., Triche, T. J., & Meshinchi, S. (2019). Long non-coding RNAs (lncRNAs) are highly associated with disease characteristics and outcome in pediatric acute myeloid leukemia - a COG and tpaml study. Blood, 134(Supplement_1), 2741–2741. https://doi.org/10.1182/blood-2019-127318
Smith, J. L., Ries, R. E., Wang, Y.-C., Leonti, A. R., Alonzo, T. A., Gamis, A. S., Aplenc, R., Kolb, A. E., Huang, B. J., Ma, X., Shaw, T. I., & Meshinchi, S. (2021). ETS family transcription factor fusions in childhood AML: Distinct expression networks and clinical implications. Blood, 138(Supplement 1), 2356–2356. https://doi.org/10.1182/blood-2021-148894
Tarlock, K., Lamble, A., Wang, J., Gerbing, R. B., Ries, R. E., Loken, M. R., Brodersen, L. E., Pardo, L., Leonti, A. R., Smith, J., Hylkema, T., Woods, W. G., Cooper, T., Kolb, E. A., Gamis, A. S., Aplenc, R., Alonzo, T., & Meshinchi, S. (2021). CEBPA bZip mutations are associated with favorable prognosis in de novo AML: A report from the childrens oncology group. Blood. https://doi.org/10.1182/blood.2020009652
Bertrums, E. J. M., Smith, J. L., Harmon, L., Ries, R. E., Wang, Y.-C. J., Alonzo, T. A., Menssen, A. J., Chisholm, K. M., Leonti, A. R., Tarlock, K., Ostronoff, F., Pogosova-Agadjanyan, E. L., Kaspers, G. J. L., Hasle, H., Dworzak, M., Walter, C., Muhlegger, N., Morerio, C., Pardo, L., … Meshinchi, S. (2023). Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica. https://doi.org/10.3324/haematol.2022.281653
Chisholm, K. M., Smith, J., Heerema-McKenney, A. E., Choi, J. K., Ries, R. E., Hirsch, B. A., Raimondi, S. C., Wang, Y.-C., Dang, A., Alonzo, T. A., Sung, L., Aplenc, R., Gamis, A. S., Meshinchi, S., & Kahwash, S. B. (2023). Pathologic, cytogenetic, and molecular features of acute myeloid leukemia with megakaryocytic differentiation: A report from the childrens oncology group. Pediatric Blood & Cancer. https://doi.org/10.1002/pbc.30251
Farrar, J. E., Smith, J. L., Othus, M., Huang, B. J., Wang, Y.-C., Ries, R., Hylkema, T., Pogosova-Agadjanyan, E. L., Challa, S., Leonti, A., Shaw, T. I., Triche, T. J., Gamis, A. S., Aplenc, R., Kolb, E. A., Ma, X., Stirewalt, D. L., Alonzo, T. A., & Meshinchi, S. (2023). Long noncoding RNA expression independently predicts outcome in pediatric acute myeloid leukemia. Journal of Clinical Oncology, 41(16), 2949–2962. https://doi.org/10.1200/jco.22.01114
Huang, B. J., Smith, J. L., Farrar, J. E., Wang, Y.-C., Umeda, M., Ries, R. E., Leonti, A. R., Crowgey, E., Furlan, S. N., Tarlock, K., Armendariz, M., Liu, Y., Shaw, T. I., Wei, L., Gerbing, R. B., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2022). Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33244-6
Huang, B. J., Smith, J. L., Wang, Y.-C., Taghizadeh, K., Leonti, A. R., Ries, R. E., Liu, Y., Kolekar, P., Tarlock, K., Gerbing, R., Crowgey, E., Furlan, S. N., Shaw, T. I., Hagiwara, K., Wei, L., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2021). CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Advances, 5(23), 4963–4968. https://doi.org/10.1182/bloodadvances.2021004965
Kappe, S., Zanghi, G., Patel, H., Camargo, N., Smith, J., Bae, Y., Hesping, E., Boddey, J., Flannery, E., Chuenchob, V., Fishbaugher, M., Mikolajczak, S., Roobsoong, W., Sattabongkot, J., Hayes, K., & Vaughan, A. (2023). Genome-wide gene expression profiles throughout human malaria parasite liver stage development. https://doi.org/10.21203/rs.3.rs-3689897/v1
Le, Q., Hadland, B., Smith, J. L., Leonti, A., Huang, B. J., Ries, R., Hylkema, T. A., Castro, S., Tang, T. T., McKay, C. N., Perkins, L., Pardo, L., Sarthy, J., Beckman, A. K., Williams, R., Idemmili, R., Furlan, S., Ishida, T., Call, L., … Meshinchi, S. (2022). CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR t cell target. Journal of Clinical Investigation, 132(22). https://doi.org/10.1172/jci157101
Noort, S., Wander, P., Alonzo, T. A., Smith, J., Ries, R. E., Gerbing, R. B., Dolman, M. E. M., Locatelli, F., Reinhardt, D., Baruchel, A., Stary, J., Molenaar, J. J., Stam, R. W., Heuvel-Eibrink, M. M. van den, Zwaan, C. M., & Meshinchi, S. (2020). The clinical and biological characteristics of NUP98-KDM5A in pediatric acute myeloid leukemia. Haematologica, haematol.2019.236745. https://doi.org/10.3324/haematol.2019.236745
Noort, S., Zimmermann, M., Reinhardt, D., Cuccuini, W., Pigazzi, M., Smith, J., Ries, R. E., Alonzo, T. A., Hirsch, B., Tomizawa, D., Locatelli, F., Gruber, T. A., Raimondi, S., Sonneveld, E., Cheuk, D. K., Dworzak, M., Stary, J., Abrahamsson, J., Arad-Cohen, N., … Zwaan, C. M. (2018). Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: A retrospective study by the i-BFM study group. Blood, 132(15), 1584–1592. https://doi.org/10.1182/blood-2018-05-849059
Smith, J. L. (2019). Consensus machine learning for gene target selection in pediatric AML risk. In biorxiv.
Smith, J. L., Ries, R. E., Farrar, J. E., Alonzo, T. A., Gerbing, R. B., Leonti, A. R., Hylkema, T. A., Gamis, A. S., Aplenc, R., Kolb, E. A., Nguyen, C., Meerzaman, D., Triche, T. J., & Meshinchi, S. (2019). Long non-coding RNAs (lncRNAs) are highly associated with disease characteristics and outcome in pediatric acute myeloid leukemia - a COG and tpaml study. Blood, 134(Supplement_1), 2741–2741. https://doi.org/10.1182/blood-2019-127318
Smith, J. L., Ries, R. E., Wang, Y.-C., Leonti, A. R., Alonzo, T. A., Gamis, A. S., Aplenc, R., Kolb, A. E., Huang, B. J., Ma, X., Shaw, T. I., & Meshinchi, S. (2021). ETS family transcription factor fusions in childhood AML: Distinct expression networks and clinical implications. Blood, 138(Supplement 1), 2356–2356. https://doi.org/10.1182/blood-2021-148894
Tarlock, K., Lamble, A., Wang, J., Gerbing, R. B., Ries, R. E., Loken, M. R., Brodersen, L. E., Pardo, L., Leonti, A. R., Smith, J., Hylkema, T., Woods, W. G., Cooper, T., Kolb, E. A., Gamis, A. S., Aplenc, R., Alonzo, T., & Meshinchi, S. (2021). CEBPA bZip mutations are associated with favorable prognosis in de novo AML: A report from the childrens oncology group. Blood. https://doi.org/10.1182/blood.2020009652