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 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.

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…

This week we’ve released 1 D. melanogaster data sets:
Celniker – 1 Computational annotation data sets
Read more…

This week we’ve released 5 D. melanogaster data sets:
Celniker – 5 RNA tiling array data sets
on the following kinds of samples:
cell lines: CME W1 Cl.8+, ML-DmBG3-c2, S2-DRSC
stages: late embryonic stage, third instar larval stage
tissues: cns-derived cell-line, dorsal mesothoracic disc, embryo-derived cell-line
Read more…

This week we’ve released 21 D. melanogaster data sets:
Lai – 1 RNA-seq (small RNAs) data sets
White – 20 ChIP-chip data sets
on the following kinds of samples:
antibodies: h3k27me3, h3k4me1, h3k4me3, h3k9ac, h3k9me3, no antibody control
stages: adult stage, embryonic stage 10, embryonic stage 11, embryonic stage 12, embryonic stage 15, embryonic stage 16, embryonic stage 17, embryonic stage 9, first instar larval stage, second instar larval stage
strains: Canton-S, y; cn bw sp
tissues: adult head, whole organism
Read more…