bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2021,
Номер
unknown
Опубликована: Сен. 10, 2021
Abstract
PomBase
(
www.pombase.org
),
the
model
organism
database
(MOD)
for
fission
yeast
Schizosaccharomyces
pombe
,
supports
research
within
and
beyond
S.
community
by
integrating
presenting
genetic,
molecular,
cell
biological
knowledge
into
intuitive
displays
comprehensive
data
collections.
With
new
content,
novel
query
capabilities,
biologist-friendly
summaries
visualisation,
also
drives
innovation
in
MOD
community.
FlyBase
provides
a
centralized
resource
for
the
genetic
and
genomic
data
of
Drosophila
melanogaster.
As
enters
our
fourth
decade
service
to
research
community,
we
reflect
on
unique
aspects
look
forward
continued
collaboration
with
larger
model
organism
communities.
In
this
study,
emphasize
dedicated
reports
tools
have
constructed
meet
specialized
needs
fly
researchers
but
also
facilitate
use
by
other
We
highlight
ways
that
support
including
an
external
resources
page,
help
resources,
multiple
avenues
which
can
interact
FlyBase.
Nucleic Acids Research,
Год журнала:
2021,
Номер
50(D1), С. D316 - D325
Опубликована: Окт. 13, 2021
Abstract
ReMap
(https://remap.univ-amu.fr)
aims
to
provide
manually
curated,
high-quality
catalogs
of
regulatory
regions
resulting
from
a
large-scale
integrative
analysis
DNA-binding
experiments
in
Human,
Mouse,
Fly
and
Arabidopsis
thaliana
for
hundreds
transcription
factors
regulators.
In
this
2022
update,
we
have
uniformly
processed
>11
000
sequencing
datasets
public
sources
across
four
species.
The
updated
Human
atlas
includes
8103
covering
total
1210
transcriptional
regulators
(TRs)
with
catalog
182
million
(M)
peaks,
while
the
reaches
4.8M
423
TRs
694
datasets.
Also,
release
is
enriched
by
two
new
Mus
musculus
Drosophila
melanogaster.
First,
Mouse
consists
123M
peaks
648
as
result
integration
validation
5503
ChIP-seq
Second,
melanogaster
contains
16.6M
550
1205
are
browsable
through
track
hubs
at
UCSC,
Ensembl
NCBI
genome
browsers.
Finally,
comes
Cis
Regulatory
Module
identification
method,
improved
quality
controls,
faster
search
results,
better
user
experience
an
interactive
tour
video
tutorials
on
browsing
filtering
catalogs.
Nucleic Acids Research,
Год журнала:
2021,
Номер
50(D1), С. D996 - D1003
Опубликована: Ноя. 10, 2021
Abstract
Ensembl
Genomes
(https://www.ensemblgenomes.org)
provides
access
to
non-vertebrate
genomes
and
analysis
complementing
vertebrate
resources
developed
by
the
project
(https://www.ensembl.org).
The
two
collectively
present
genome
annotation
through
a
consistent
set
of
interfaces
spanning
tree
life
presenting
sequence,
annotation,
variation,
transcriptomic
data
comparative
analysis.
Here,
we
our
largest
increase
in
plant,
metazoan
fungal
since
project's
inception
creating
one
world's
most
comprehensive
genomic
describe
efforts
reduce
redundancy
Bacteria
portal.
We
detail
new
gene
emerging
support
for
pangenome
analysis,
accelerate
dissemination
Rapid
Release
resource
AlphaFold
visualization.
Finally,
details
future
plans
including
updates
on
integration
with
Ensembl,
how
plan
improve
microbial
research
community.
Software
are
made
available
without
restriction
via
website,
online
tools
platform
programmatic
(available
under
an
Apache
2.0
license).
Data
synchronised
Ensembl's
release
cycle.
Nucleic Acids Research,
Год журнала:
2021,
Номер
50(D1), С. D1255 - D1261
Опубликована: Окт. 19, 2021
The
Human
Disease
Ontology
(DO)
(www.disease-ontology.org)
database,
has
significantly
expanded
the
disease
content
and
enhanced
our
userbase
website
since
DO's
2018
Nucleic
Acids
Research
DATABASE
issue
paper.
Conservatively,
based
on
available
resource
statistics,
terms
from
DO
have
been
annotated
to
over
1.5
million
biomedical
data
elements
citations,
a
10×
increase
in
past
5
years.
DO,
funded
as
NHGRI
Genomic
Resource,
plays
key
role
knowledge
organization,
representation,
standardization,
serving
reference
framework
for
multiscale
integration
analysis
across
thousands
of
clinical,
computational
research
projects
genomic
resources
around
world.
This
update
reports
addition
1,793
new
terms,
14%
textual
definitions
22
137
SubClassOf
axioms
defining
connections
representing
complex
classification.
updated
provides
multifaceted
etiology
searching,
documentation
educational
resources.
Nucleic Acids Research,
Год журнала:
2021,
Номер
50(D1), С. D1040 - D1045
Опубликована: Ноя. 8, 2021
Abstract
Insects
are
the
largest
group
of
animals
on
planet
and
have
a
huge
impact
human
life
by
providing
resources,
transmitting
diseases,
damaging
agricultural
crop
production.
Recently,
large
amount
insect
genome
gene
data
has
been
generated.
A
comprehensive
database
is
highly
desirable
for
managing,
sharing,
mining
these
resources.
Here,
we
present
an
updated
database,
InsectBase
2.0
(http://v2.insect-genome.com/),
covering
815
genomes,
25
805
transcriptomes
>16
million
genes,
including
15
045
111
coding
sequences,
3
436
022
3′UTRs,
4
345
664
5′UTRs,
112
162
miRNAs
1
293
430
lncRNAs.
In
addition,
used
in-house
standard
pipeline
to
annotate
434
653
genes
belonging
164
families;
215
986
potential
horizontally
transferred
genes;
419
KEGG
pathways.
Web
services
such
as
BLAST,
JBrowse2
Synteny
Viewer
provided
searching
visualization.
serves
valuable
platform
entomologists
researchers
in
related
communities
animal
evolution
invertebrate
comparative
genomics.
Abstract
FlyBase
(flybase.org)
is
a
model
organism
database
and
knowledge
base
about
Drosophila
melanogaster,
commonly
known
as
the
fruit
fly.
Researchers
from
around
world
rely
on
genetic,
genomic,
functional
information
available
in
FlyBase,
well
its
tools
to
view
interrogate
these
data.
In
this
article,
we
describe
latest
developments
updates
FlyBase.
These
include
introduction
of
single-cell
RNA
sequencing
data,
improved
content
display
information,
updated
orthology
pipelines,
new
chemical
reports,
enhancements
our
outreach
resources.
Since
1999,
The
Arabidopsis
Information
Resource
(www.arabidopsis.org)
has
been
curating
data
about
the
thaliana
genome.
Its
primary
focus
is
integrating
experimental
gene
function
information
from
peer-reviewed
literature
and
codifying
it
as
controlled
vocabulary
annotations.
Our
goal
to
produce
a
"gold
standard"
functional
annotation
set
that
reflects
current
state
of
knowledge
At
same
time,
resource
serves
nexus
for
community-based
collaborations
aimed
at
improving
quality,
access,
reuse.
For
past
decade,
our
work
made
possible
by
subscriptions
global
user
base.
This
update
covers
ongoing
biocuration
work,
some
modernization
efforts
contribute
first
major
infrastructure
overhaul
since
2011,
introduction
JBrowse2,
resource's
role
in
community
activities
such
organizing
structural
reannotation
assessment,
we
used
ontology
annotations
metric
evaluate:
(1)
what
currently
known
(2)
"unknown"
genes.
Currently,
74%
proteome
annotated
least
one
term.
Of
those
loci,
half
have
support
following
aspects:
molecular
function,
biological
process,
or
cellular
component.
sheds
light
on
genes
which
not
yet
identified
any
published
no
annotation.
Drawing
attention
these
unknown
highlights
gaps
potential
sources
novel
discoveries.
Nature Genetics,
Год журнала:
2024,
Номер
56(4), С. 686 - 696
Опубликована: Март 11, 2024
Abstract
To
regulate
expression,
enhancers
must
come
in
proximity
to
their
target
gene.
However,
the
relationship
between
timing
of
enhancer–promoter
(E–P)
and
activity
remains
unclear,
with
examples
uncoupled,
anticorrelated
correlated
interactions.
assess
this,
we
selected
600
characterized
or
promoters
tissue-specific
Drosophila
embryos
performed
Capture-C
FACS-purified
myogenic
neurogenic
cells
during
specification
tissue
differentiation.
This
enabled
direct
comparison
E–P
transitioning
from
OFF-to-ON
ON-to-OFF
states
across
developmental
conditions.
showed
remarkably
similar
topologies
specified
muscle
neuronal
cells,
which
are
uncoupled
activity.
During
differentiation,
many
new
distal
interactions
emerge
where
changes
reflect
The
mode
regulation
therefore
appears
change
as
embryogenesis
proceeds,
largely
permissive
cell-fate
more
instructive
terminal
when
is
coupled
activation.
