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Bioinformatics Tools

Pollen RCN members and collaborators have created bioinformatic and database visualization tools you may find useful in your research.

Bioinformatics tools


The Pollen Transcriptome Navigator, which presents data from pollen microarray experiments, focusing on data from the ATH1 expression array for Arabidopsis thaliana. Use this tool to visualize how your gene (or genes) of interest change their pattern of expression from pollen grain development to pollen tube growth (in vitro and in vivo). This tool can identify i) genes specifically or preferentially expresed in pollen, ii) members of a gene family highly expressed in pollen, iii) genes that are regulated by pollen development and by tube growth, and iv) genes that are up- or down-regulated in pollen tubes by in vivo cues from female tissues after pollination.

Please send comments and suggestions to Heven Sze.

Integrated Genome Browser, which presents data from RNA-Seg, tiling array, and other large-scale genomic data sets. To assist researchers interested in reproductive development in plants, we added a maize reproductive biology RNA-Seq data set (Study Accession SRP006463) to the IGB system. These data feature short read alignments isolated from 14 maize reproductive tissues and were first published in this article from the journal Plant Genome.

Go to:

IGB Tutorial: RNA-Seq data from maize reproductive tissues

IGB User's Guide

Please send comments and suggestions to Ann Loraine.

Pollen Tube Tracker. This module automatically tracks multiple, overlapping, fluorescent pollen tube trajectories in a time-lapse image. Authors: Ernesto Brau, Andrew Predoehl, Kobus Barnard, Salika Dunatunga, and Ravi Palanivelu at the University of Arizona.

This tracker first processes a 4D image and looks for differences between successive time steps. It finds "spots" of connected pixels from 5 to 50 pixels across. The spots become the input to a MCMCDA tracker (Markov chain, Monte Carlo data association) which infers the number of tracks and the position of the tracks (as a polygonal path) that could have generated the spots.

Please send comments and suggestions to Ravi Palanivelu.

Heat Tree Viewer - An exciting new tool to analyze gene families by integrating gene expression data with phylogeny

The Heat Tree Viewer allows users to analyze a gene family by displaying gene expression data from a comprehensive collection of cell types/tissues, including pollen and other key reproductive cell types, with a phylogentic tree. The output is a gene expression heat map in the context of a phylogenetic tree, or Heat Tree. Brown University students working with the Johnson and DeLong labs developed this tool with support from the Howard Hughes Medical Institute.

Questions, contact Mark Johnson: mark_johnson_1@brown.edu

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