modENCODE |  Help

Welcome to modMine

The modENCODE project aims to identify all sequence-based functional elements in the C. elegans and D. melanogaster genomes. modENCODE labs submit data to the Data Coordination Center (DCC) where we organize and present the results.

modMine is an integrated web resource of data & tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser. Explore some of the tools provided below and check out our quick start guide

Please cite modMine if it helped your research!

modMine release 33 28JUL2014 uses genome annotations 5.54 for fly and 220 for worm.



Enter names, identifiers or keywords for genes, proteins, pathways, ontology terms, etc. (e.g. zen, pha-4, DNA-binding).

Or search modENCODE experiments by type, lab name, antibody, etc. (e.g. ChIP-seq, Snyder, CP190).

Genomic Region Search

Genome Region Search Explore a genomic region for features found by the modENCODE project. Genomic Region Search

Fly Gene Expression

Fly expression heatmap

View an expression score heatmap for any list of fly genes. See an example.

To upload your own list of genes, use the form above or go to the 'Lists' tab and click on 'Upload' to create and name the new list. You can also use any of modMine's queries to create a list.

Fly Chromatin states

flyscoreGBrowse Ideograms

parklabviewerPark Lab Viewer

Includes folded view and also data about DHS, TSS, replication, etc.

Regulatory Network

Worm Regulatory Network
Fly Regulatory Network

Explore an hierarchical view of the physical regulatory networks.

Upload Lists


Enter a list of identifiers.


Use Template Queries


Get started with powerful queries using our predefined searches. These customizable templates have been designed around common tasks performed by our biologist community.

To see how they work, why not try a template from our examples page?


Analyze Lists of Data


widget charts Explore and Analyze. Upload lists of identifiers to use in queries and discover relationshops in our analysis widgets. See an example.