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:
| D. mojavensis |
4 |
| D. pseudoobscura |
4 |
| D. simulans |
4 |
| D. ananassae |
1 |
| D. virilis |
1 |
| D. yakuba |
1 |
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:
| D. melanogaster |
1037 |
| C. elegans |
410 |
| D. mojavensis |
2 |
| D. pseudoobscura |
2 |
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:
| D. melanogaster |
870 |
| C. elegans |
346 |
| D. mojavensis |
2 |
| D. pseudoobscura |
2 |
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.
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.
This week we’ve released 24 C. elegans data sets:
Lieb – 7 ChIP-chip data sets
Waterston – 17 RNA tiling array data sets
on the following kinds of samples:
antibodies: dpy-27, no antibody control, rna polii ctd domain unphosophorylated, sdc-2, sdc-3, trimethylated lys-9 on histone h3
stages: blastula embryo, elongating embryo, embryo, enclosing embryo, fully-elongated embryo, gastrulating embryo, l1 larva, l2 larva, l3 larva, l4 larva, l4 larva male, late cleavage stage embryo, newly molted young adult hermaphrodite
strains: 11dh, CB4689, JK1107, N2, YPT41, YPT47
tissues: hermaphrodite gonad, whole organism
Read more…
This week we’ve released 2 C. elegans data sets:
Lieb – 2 ChIP-chip data sets
on the following kinds of samples:
antibodies: dpy-27, no antibody control, rna polii ctd domain unphosophorylated
stage: l4 larva
strain: N2
tissue: whole organism
Read more…
This week we’ve released 7 C. elegans data sets:
Waterston – 7 RNA-seq data sets
on the following kinds of samples:
stages: adult male, embryo, l1 larva, l2 larva, l3 larva, l4 larva, newly molted young adult hermaphrodite
strains: CB4689, N2
tissue: whole organism
Read more…
This week we’ve released 4 C. elegans data sets:
Lieb – 4 ChIP-chip data sets
on the following kinds of samples:
antibodys: dpy-27, htz-1, no antibody control, rna polii ctd domain unphosophorylated, sdc-3
stage: embryo
strain: N2
tissue: whole organism
Read more…
This week we’ve released 7 C. elegans data sets:
Snyder – 7 ChIP-seq data sets
on the following kinds of samples:
antibodys: daf-16, pha-4, RNA pol II
stages: embryo, l1 larva, l4 larva, l4-adult molt, newly molted young adult hermaphrodite
strains: OP37, TJ356
tissue: whole organism
Read more…
This week we’ve released 8 C. elegans data sets:
Lieb – 3 ChIP-chip data sets
Snyder – 5 ChIP-seq data sets
on the following kinds of samples:
antibodies: ama-1, dpy-27, mab-5, pha-4, sdc-3, RNA Polymerase II
stages: embryo, l3 larva, l4 larva, l4-adult molt, newly molted young adult hermaphrodite
strains: N2, OP26, OP34, OP37
tissue: whole organism
Read more…