modENCODE Blog

modMine release 25

Release 25 of modMine contains all the submissions validated by the end of August 2011. There are 1664 submissions, organised in 69 experiments which in turn are divided in 12 categories.

There are 1185 submissions regarding D. melanogaster, 464 concern C. elegans, and there is also a small number of submssions for other Drosophila species:

New in this release.

- Ensembl Compara

The Ensembl Compara data set has been used to get homologues information.

- Easier exploration of other mines

Links to other mines (RatMine, FlyMine, metabolicMine,ZFINMine, YeastMine)  are available on reposrt and list report pages and allows exploration of orthologues genes.

modMine release 24

Release 24 of modMine contains all the submissions validated by the end of June 2011. There are 1504 submissions, organised in 61 experiments which in turn are divided in 12 categories.

New in this release.

- A new way of managing users’ lists when transferring them from one release to the next one. The new system makes transparent to the user any update made necessary by the changes on elements of the list in the model organism databases (FlyBase or WormBase).

Usually there will be no changes and no action will need to be taken.  However, if a user’s list needs upgrading, these simple steps need to be followed:

• log in
• go to the “My Mine” section of modMine
• check the status of your lists by visiting the “Lists” page (http://intermine.modencode.org/query/mymine.do).
• Click on the “Upgrade” links that you find in the last column of the table and resolve duplications and conflicts.

The new system allows also a much shorter downtime of modMine when the release is changed.

- Sequence features can be exported as a file or sent to Galaxy in UCSC BED format

- Data labels and column names are configurable now and not tied to the database field names.

modMine release 23

Release 23 of modMine contains all the submissions validated by the end of April 2011. There are 1451 submissions, organised in 61 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:

• All the worm data has been updated to genomic version 220
• New display for the content pages, allowing a more compact overview of the data available

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.

This February Data Coordination Center for modENCODE starts having regular User Group webinars using WebEx teleconference services. The goal of these webinars is to provide better understanding and facilitate analyses of the data generated by modENCODE project. The updated schedule is going to be available at DCC Wiki (people outside modENCODE project may use anonymous login to view the page). Webinars are run between 12 and 1pm every first Thursday of the month, with the first webinar ‘Understanding worm and fly chromatin modification data‘ scheduled for February 3rd. Gary Karpen and researchers from Jason Lieb’s group will be available for questions. This online webinar will introduce participants to the chromatin IP data, and describe how to visualize and download it from the modENCODE web site. Space is limited so advance registration is necessary. Please email help@modencode.org to reserve your spot. Instruction on how to log in to WebEx conference and dial-in information for audio part are provided along with the schedule.

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

These two tables provide estimated expression levels for annotated genes and exons, using signals from Affymetrix Drosophila tiling arrays. The arrays were hybridized with total RNAs extracted from 25 cell lines and 30 developmental stages.

Drosophila_Cell_Lines_and_Developmental_Stages_Exon_Scores.txt
Drosophila_Cell_Lines_and_Developmental_Stages_Gene_Scores.txt

For more information, please see http://www.modencode.org/docs/flyscores.

The tables were compiled by the Bloomington group in the fly transcriptome project of modENCODE (Celniker, PI).

modMine release 15

New full release with 770 submissions. 568 concern fly, 202 worm.

This release contains a snapshot of all fly and worm data for analysis (data analysis freeze).

Please note that the submissions for fly of the Henikoff group have been updated respect release 14. The update has increased the number of submissions by 8.

A set of fly data has been frozen for analysis. It comprises 560 submissions and bulk downloads of the data are available from the Download Site.
The modMine data warehouse will be available shortly.

This week we’ve released 1 D. melanogaster data sets:
White – 1 ChIP-chip data sets
on the following kinds of samples:
antibodys: h3k9ac, no antibody control
stage: pupal stage
strain: y; cn bw sp
tissue: whole organism
Read more…