modENCODE Blog

modMine release 22

Release 22 of modMine contains 1220 submissions, organised in 57 experiments which in turn are divided in 14 categories. The break down of the number of submissions in term of organism is the following:

New in this release:

• Network displayer for the Worm Regulatory Network, where you explore the network and access reports on all the genes involved. The network displayer enliven the graph of Figure 3 in the paper “Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. (2010) Science 330: 1775-1787. [DOI:10.1126/science.1196914]“
• Now features of the type ‘binding site’ are associated to their source file, i.e. the submitted file containing the given feature. When in a submission this type of features derive form more than a single data file, they are displayed also in the summaries.

The following modENCODE publications were published online on December 22, 2010 (the two integrative analysis papers are in the Dec. 24th issue of Science).

Gerstein MB et al., Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. (2010) Science 330: 1775-1787. Published online 22 December 2010 [DOI:10.1126/science.1196914]

The modENCODE Consortium et al., Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. (2010) Science 330: 1787-1797. Published online 22 December 2010 [DOI:10.1126/science.1198374]

Allen MA, Hillier LW, Waterston RH, Blumenthal T.  A global analysis of C. elegans trans-splicing. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.113811.110

Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. gr.116657.110; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, et al. The transcriptional diversity of 25 drosophila cell lines. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.112961.110

Chung W, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC. Computational and experimental identification of mirtrons in Drosophila melanogaster and caenorhabditis elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.113050.110

Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the drosophila replication program. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.116038.110

Ercan S, Lubling Y, Segal E, Lieb JD. High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.115931.110

Graveley BR, et al., The developmental transcriptome of Drosophila melanogaster. (2010) Nature DOI: doi:10.1038/nature09715 Published online 22 December 2010

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.112466.110

Kharchenko PV, et al., Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. (2010) Nature DOI: doi:10.1038/nature09725 Published online 22 December 2010

Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung M, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.115519.110

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, et al. Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data. Genome Res. gr.110189.110; Published in Advance December 22, 2010, doi:10.1101/gr.110189.110

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.114587.110

Nordman J, Li S, Eng T, MacAlpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Res. Published in Advance December 22, 2010, doi:10.1101/gr.114611.110

Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, et al. Plasticity in patterns of histone modifications and chromosomal proteins in drosophila heterochromatin. Genome Res. gr.110098.110; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen SC, Sreedharan VT, Widmer C, Jo J, et al. A spatial and temporal map of C. elegans gene expression. Genome Res. gr.114595.110; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110

Supplementary materials and links accessing modencode data used in the analysis for the upcoming Science papers can be found at

http://www.modencode.org/publications/integrative_fly_2010/

http://www.modencode.org/publications/integrative_worm_2010/

A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.

Nucleic Acids Res. 2009 Dec 4. [Epub ahead of print]
Ooi SL, Henikoff JG, Henikoff S.
PMID: 19966274

The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence.

Curr Biol. 2009 Nov 17;19(21):1777-87. Epub 2009 Oct 22.
Ercan S, Dick LL, Lieb JD.
PMID: 19853451