NOJAH: Not Just Another Heatmap for Genome-Wide Cluster Analysis

Abstract

23Since their inception, several tools have been developed for cluster analysis and 24 heatmap construction. The application of such tools to the number and types of genome-25 wide data available from next generation sequencing (NGS) technologies requires the 26 adaptation of statistical concepts, such as in defining a most variable gene set, and more 27 intricate cluster analyses method to address multiple omic data types. Additionally, the 28 growing number of publicly available datasets has created the desire to estimate the 29 statistical significance of a gene signature derived from one dataset to similarly group 30 samples based on another dataset. The currently available number of tools and their 31 combined use for generating heatmaps, along with the several adaptations of statistical 32 concepts for addressing the higher dimensionality of genome-wide NGS-derived data, 33 has created a further challenge in the ability to replicate heatmap results. We introduce 34 NOJAH (NOt Just Another Heatmap), an interactive tool that defines and implements a 35 workflow for genome-wide cluster analysis and heatmap construction by creating and 36 combining several tools into a single user interface. NOJAH includes several newly 37 developed scripts for techniques that though frequently applied are not sufficiently 38 documented to allow for replicability of results. These techniques include: defining a most 39 variable gene set (a.k.a., 'core genes'), estimating the statistical significance of a gene 40 signature to separate samples into clusters, and performing a result merging integrated 41 cluster analysis. With only a user uploaded dataset, NOJAH provides as output, among 42 other things, the minimum documentation required for replicating heatmap results. 43 Additionally, NOJAH contains five different existing R packages that are connected in the 44 interface by their functionality as part of a defined workflow for genome-wide cluster 45 analysis. The NOJAH application tool is available at 46

Epigenetically heterogeneous tumor cells direct collective invasion through filopodia-driven fibronectin micropatterning

“…Data were log 2(normalized count + 1)-transformed for all downstream analysis. Unsupervised hierarchical clustering and the resulting heat maps were created using NOt Just Another Heatmap (57).…”

Host Genome Variation is Associated with Neurocognitive Outcome in Survivors of Pediatric Medulloblastoma

“…Unsupervised (within the context of samples) hierarchical agglomerative heatmap clustering using the original variant proportions was carried out using euclidean distance and ward.D clustering. Heatmap clustering analysis was conducted using NOJAH [23].…”

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Medoid-based Clustering pada Kecamatan di Kabupaten Lebak dan Pandeglang Provinsi Banten Berdasarkan Trilogi Ketahanan Pangan

“…Hasil kluster dengan jarak Euclidean, squared Euclidean, dan Manhattan divalidasi dengan consensus clustering (Monti et al, 2003;Rupji et al, 2019) Gambar 6 menunjukkan bahwa analisis kluster menghasilkan kluster 3 (38%) dengan karakteristik bernilai rendah pada ketiga variabel (kluster rawan). Kluster 1 (16%) adalah kluster ketersediaan dan akses karena anggota kluster memiliki nilai yang tinggi pada kedua variabel tersebut.…”