README:

Identification of Functional Elements and Regulatory Circuits by
Drosophila modENCODE
    
The modENCODE Consortium, Sushmita Roy, Jason Ernst, Peter
V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane
M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan
Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas
Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov,
Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian
Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael
Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri,
Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael
O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja
G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John
Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara
K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy
E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David
Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu,
Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad,
Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent,
Lucy Cherbas, Sarah C. R. Elgin, Thomas R. Gingeras, Robert Grossman,
Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda,
Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James
W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton
R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park,
Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David
M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis, David
Acevedo, Richard Auburn, Galt Barber, Hugo J. Bellen, Eric P. Bishop,
Terri D. Bryson, Aurelien Chateigner, Jia Chen, Hiram Clawson, Charles
L. G. Comstock, Sergio Contrino, Leyna C. DeNapoli, Queying Ding, Alex
Dobin, Marc H. Domanus, Jorg Drenkow, Sandrine Dudoit, Jackie Dumais,
Thomas Eng, Delphine Fagegaltier, Sarah E. Gadel, Srinka Ghosh,
Francois Guillier, David Hanley, Gregory J. Hannon, Kasper D. Hansen,
Elizabeth Heinz, Angie S. Hinrichs, Martin Hirst, Sonali Jha, Lichun
Jiang, Youngsook L. Jung, Helena Kashevsky, Cameron D. Kennedy, Ellen
T. Kephart, Laura Langton, Ok-Kyung Lee, Sharon Li, Zirong Li, Wei
Lin, Daniela Linder-Basso, Paul Lloyd, Rachel Lyne, Sarah
E. Marchetti, Marco Marra, Nicolas R. Mattiuzzo, Sheldon McKay, Folker
Meyer, David Miller, Steven W. Miller, Richard A. Moore, Carolyn
A. Morrison, Joseph A. Prinz, Michelle Rooks, Richard Moore, Kim
M. Rutherford, Peter Ruzanov, Douglas A. Scheftner, Lionel
Senderowicz, Parantu K. Shah, Gregory Shanower, Richard Smith,
E. O. Stinson, Sarah Suchy, Aaron E. Tenney, Feng Tian, Koen
J. T. Venken, Huaien Wang, Robert White, Jared Wilkening, Aarron
T. Willingham, Chris Zaleski, Zheng Zha, Dayu Zhang, Yongjun Zhao,
Jennifer Zieba
    

Identification of Functional Elements and Regulatory Circuits by <i>Drosophila</i> modENCODE
DP - 2010
Science 2010-12-24 330(6012): 1787-1797
DOI - 10.1126/science.1198374 [doi]
PMID - 21177974
https://www.science.org/doi/abs/10.1126/science.1198374

For biologists, having a genome in hand is only the beginning—much
more investigation is still needed to characterize how the genome is
used to help to produce a functional organism (see the Perspective by
Blaxter). In this vein, Gerstein et al. (p. 1775) summarize for the
Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787)
summarize for the Drosophila melanogaster genome, full transcriptome
analyses over developmental stages, genome-wide identification of
transcription factor binding sites, and high-resolution maps of
chromatin organization. Both studies identified regions of the
nematode and fly genomes that show highly occupied targets (or HOT)
regions where DNA was bound by more than 15 of the transcription
factors analyzed and the expression of related genes were
characterized. Overall, the studies provide insights into the
organization, structure, and function of the two genomes and provide
basic information needed to guide and correlate both focused and
genome-wide studies. The Drosophila modENCODE project demonstrates the
functional regulatory network of flies. To gain insight into how
genomic information is translated into cellular and developmental
programs, the Drosophila model organism Encyclopedia of DNA Elements
(modENCODE) project is comprehensively mapping transcripts, histone
modifications, chromosomal proteins, transcription factors,
replication proteins and intermediates, and nucleosome properties
across a developmental time course and in multiple cell lines. We have
generated more than 700 data sets and discovered protein-coding,
noncoding, RNA regulatory, replication, and chromatin elements, more
than tripling the annotated portion of the Drosophila
genome. Correlated activity patterns of these elements reveal a
functional regulatory network, which predicts putative new functions
for genes, reveals stage- and tissue-specific regulators, and enables
gene-expression prediction. Our results provide a foundation for
directed experimental and computational studies in Drosophila and
related species and also a model for systematic data integration
toward comprehensive genomic and functional annotation.



DataS1.txt	Listing of all modENCODE data sets and accession numbers
DataS2.txt	Novel transcripts with complete or incomplete conserved ORFs
DataS3.gff	Noncoding RNA-seq transcripts with conserved RNA secondary structure
DataS4.gff	Novel promoter predictions based on chromatin signatures
DataS5.zip	Genome annotated using the 9-state chromatin model
DataS6.zip	Genome annotated using the 30-state chromatin model
DataS7.zip	Predicted TFBS
DataS8.gff	HOT regions
DataS9.txt	Machine-parseable version of ChIP-based physical regulatory network (pRN) combined with miRNA regulations
DataS10.xls	Summary of connectivity properties of pRN
DataS11.zip	Lists of all motif instances for the 8 motifs shown in Figure 7B
DataS12.gff	Feature-specific data sets for functional network reconstruction
DataS13.gff	Functional regulatory network
DataS14.tgz	Gene co-expression clusters
DataS15.zip	Function prediction of all genes
DataS16.txt	Genes predicted as regulators of key developmental events
DataS17.tgz	Gene expression model based on regulator binding


Extra files found together with the above.
S14.tgz
S15.tgz
FRNDatasets.zip
predmodel.tgz
