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Citations per year

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Tool usage distribution map

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chevron_left Gene expression microarray data visualization Gene expression visualization chevron_right
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TreeView specifications


Unique identifier OMICS_01574
Name TreeView
Alternative names Java Treeview, JavaTreeView
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 1.1.6
Stability Stable
Maintained Yes




No version available



  • person_outline Alok Saldanha

Publications for TreeView


Java Treeview—extensible visualization of microarray data.

2004 Bioinformatics
DOI: 10.1093/bioinformatics/bth349

TreeView citations


Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

Nat Commun
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w
call_split See protocol

[…] stered (similarity metric: correlation (uncentered), clustering method: average linkage) using the version 3.0 of Cluster (open source clustering software), and visualized with the Java-based program TreeView, in order to assess similarities and differences among their expression patterns. Here and in other heat maps utilized, genes with a null normalized expression value are log-transformed and, […]


STT3 dependent PD L1 accumulation on cancer stem cells promotes immune evasion

Nat Commun
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6
call_split See protocol

[…] he genes in the “epithelial” arm (Supplementary Data ). A higher EMT score indicates a more mesenchymal-like signature. To view the clustering results generated by Cluster 3.0, we use Alok Saldanha’s Java TreeView [], which can display both hierarchical and k-means clustering results. The heat map was represented graphically by coloring each samples on the […]


Effect of Bmi1 over expression on gene expression in adult and embryonic murine neural stem cells

Sci Rep
PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] Cuffdiff at the Galaxy server,. Further analysis was performed using Excel. Clustering was performed using Cluster 3.0 ( and visualized using Java Treeview ( Gene ontology analysis was performed using the Generic Gene Ontology Term Finder. For comparison with other data sets, data was downloaded or obtaine […]


Correlation Analyses Reveal a Limited Role of Transcription in Genome Wide Differential MicroRNA Expression in Mammals

Front Genet
PMCID: 5946028
PMID: 29780403
DOI: 10.3389/fgene.2018.00154

[…] IP-seq signals, between miRNA expression and mRNA expression, and between the duplicate datasets ().Hierarchical clustering was performed using the Cluster 3.0 program (; ), and results visualized by TreeView (). […]


Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors

BMC Genomics
PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] llis one-way ANOVA test with Dunn’s correction for multiple comparisons. Z values were hierarchically clustered using Cluster 3.0 [] according to species and graphically represented as heatmaps using Java TreeView 1.1.6r4 ( study protein sequence divergence according to more specific GO terms, the whole set of GO 1:1 orthologs (isotig-dataset) was subdivided int […]


Comprehensive gene expression analysis of canine invasive urothelial bladder carcinoma by RNA Seq

BMC Cancer
PMCID: 5921755
PMID: 29699519
DOI: 10.1186/s12885-018-4409-3
call_split See protocol

[…] ion for each gene) were used to adjust for abundance differences across samples, and differentially expressed genes (DEGs) were extracted. The normalized gene counts were imported into Cluster3.0 and Java TreeView (version 1.1.6r4) for hierarchical clustering analysis and visualization. Enriched pathway and functional classification analyses of differences in expression of DEGs were performed usin […]

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TreeView institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
TreeView funding source(s)
Supported by a National Defense Science and Engineering Graduate Fellowship, the Stanford Genome Training Program (Training Grant NIH 5 T32 HG00044) and NIH grants HG 01315 and GM 46406.

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