Nature Communications,
Journal Year:
2025,
Volume and Issue:
16(1)
Published: Jan. 8, 2025
Abstract
Post-translational
modifications
(PTMs)
play
pivotal
roles
in
regulating
cellular
signaling,
fine-tuning
protein
function,
and
orchestrating
complex
biological
processes.
Despite
their
importance,
the
lack
of
comprehensive
tools
for
studying
PTMs
from
a
pathway-centric
perspective
has
limited
our
ability
to
understand
how
modulate
pathways
on
molecular
level.
Here,
we
present
PTMNavigator,
tool
integrated
into
ProteomicsDB
platform
that
offers
an
interactive
interface
researchers
overlay
experimental
PTM
data
with
pathway
diagrams.
PTMNavigator
provides
~3000
canonical
manually
curated
databases,
enabling
users
modify
create
custom
diagrams
tailored
data.
Additionally,
automatically
runs
kinase
enrichment
algorithms
whose
results
are
directly
visualization.
This
view
intricate
relationship
between
signaling
pathways.
We
demonstrate
utility
by
applying
it
two
phosphoproteomics
datasets,
showing
can
enhance
analysis,
visualize
drug
treatments
result
discernable
flow
PTM-driven
aid
proposing
extensions
existing
By
enhancing
understanding
dynamics
facilitating
discovery
PTM-pathway
interactions,
advances
knowledge
biology
its
implications
health
disease.
The Innovation,
Journal Year:
2021,
Volume and Issue:
2(3), P. 100141 - 100141
Published: July 1, 2021
Public
summary•clusterProfiler
supports
exploring
functional
characteristics
of
both
coding
and
non-coding
genomics
data
for
thousands
species
with
up-to-date
gene
annotation•It
provides
a
universal
interface
annotation
from
variety
sources
thus
can
be
applied
in
diverse
scenarios•It
tidy
to
access,
manipulate,
visualize
enrichment
results
help
users
achieve
efficient
interpretation•Datasets
obtained
multiple
treatments
time
points
analyzed
compared
single
run,
easily
revealing
consensus
differences
among
distinct
conditionsSummaryFunctional
analysis
is
pivotal
interpreting
high-throughput
omics
life
science.
It
crucial
this
type
tool
use
the
latest
databases
as
many
organisms
possible.
To
meet
these
requirements,
we
present
here
an
updated
version
our
popular
Bioconductor
package,
clusterProfiler
4.0.
This
package
has
been
enhanced
considerably
its
original
published
9
years
ago.
The
new
based
on
internally
supported
ontologies
pathways
well
provided
by
or
derived
online
databases.
also
extends
dplyr
ggplot2
packages
offer
interfaces
operation
visualization.
Other
features
include
set
comparison
lists.
We
anticipate
that
4.0
will
wide
range
scenarios
across
organisms.Graphical
abstract
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
51(W1), P. W207 - W212
Published: May 5, 2023
g:Profiler
is
a
reliable
and
up-to-date
functional
enrichment
analysis
tool
that
supports
various
evidence
types,
identifier
types
organisms.
The
toolset
integrates
many
databases,
including
Gene
Ontology,
KEGG
TRANSFAC,
to
provide
comprehensive
in-depth
of
gene
lists.
It
also
provides
interactive
intuitive
user
interfaces
ordered
queries
custom
statistical
backgrounds,
among
other
settings.
multiple
programmatic
access
its
functionality.
These
can
be
easily
integrated
into
workflows
external
tools,
making
them
valuable
resources
for
researchers
who
want
develop
their
own
solutions.
has
been
available
since
2007
used
analyse
millions
queries.
Research
reproducibility
transparency
are
achieved
by
maintaining
working
versions
all
past
database
releases
2015.
849
species,
vertebrates,
plants,
fungi,
insects
parasites,
any
organism
through
user-uploaded
annotation
files.
In
this
update
article,
we
introduce
novel
filtering
method
highlighting
Ontology
driver
terms,
accompanied
new
graph
visualizations
providing
broader
context
significant
terms.
As
leading
list
interoperability
service,
offers
resource
genetics,
biology
medical
researchers.
freely
accessible
at
https://biit.cs.ut.ee/gprofiler.
Contemporary
bioinformatic
and
chemoinformatic
capabilities
hold
promise
to
reshape
knowledge
management,
analysis
interpretation
of
data
in
natural
products
research.
Currently,
reliance
on
a
disparate
set
non-standardized,
insular,
specialized
databases
presents
series
challenges
for
access,
both
within
the
discipline
integration
interoperability
between
related
fields.
The
fundamental
elements
exchange
are
referenced
structure-organism
pairs
that
establish
relationships
distinct
molecular
structures
living
organisms
from
which
they
were
identified.
Consolidating
sharing
such
information
via
an
open
platform
has
strong
transformative
potential
research
beyond.
This
is
ultimate
goal
newly
established
LOTUS
initiative,
now
completed
first
steps
toward
harmonization,
curation,
validation
dissemination
750,000+
pairs.
hosted
Wikidata
regularly
mirrored
https://lotus.naturalproducts.net
.
Data
framework
broadens
access
interoperability,
opening
new
possibilities
community
curation
evolving
publication
models.
Furthermore,
embedding
into
vast
graph
will
facilitate
biological
chemical
insights.
initiative
represents
important
advancement
design
deployment
comprehensive
collaborative
base.
Nature,
Journal Year:
2022,
Volume and Issue:
613(7942), P. 169 - 178
Published: Dec. 21, 2022
Abstract
Tissue
regeneration
requires
coordination
between
resident
stem
cells
and
local
niche
1,2
.
Here
we
identify
that
senescent
are
integral
components
of
the
skeletal
muscle
regenerative
repress
at
all
stages
life.
The
technical
limitation
senescent-cell
scarcity
3
was
overcome
by
combining
single-cell
transcriptomics
a
enrichment
sorting
protocol.
We
identified
isolated
different
cell
types
from
damaged
muscles
young
old
mice.
Deeper
transcriptome,
chromatin
pathway
analyses
revealed
conservation
identity
traits
as
well
two
universal
senescence
hallmarks
(inflammation
fibrosis)
across
type,
time
ageing.
Senescent
create
an
aged-like
inflamed
mirrors
inflammation
associated
with
ageing
(inflammageing
4
)
arrests
proliferation
regeneration.
Reducing
burden
cells,
or
reducing
their
inflammatory
secretome
through
CD36
neutralization,
accelerates
in
By
contrast,
transplantation
delays
Our
results
provide
technique
for
isolating
vivo
define
blueprint
muscle,
uncover
unproductive
functional
interactions
niches
can
be
overcome.
As
also
accumulate
human
muscles,
our
findings
open
potential
paths
improving
repair
throughout
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
52(D1), P. D679 - D689
Published: Nov. 6, 2023
WikiPathways
(wikipathways.org)
is
an
open-source
biological
pathway
database.
Collaboration
and
open
science
are
pivotal
to
the
success
of
WikiPathways.
Here
we
highlight
continuing
efforts
supporting
WikiPathways,
content
growth
collaboration
among
researchers.
As
evolving
database,
there
a
growing
need
for
address
overcome
technical
challenges.
In
this
direction,
has
undergone
major
restructuring,
enabling
renewed
approach
sharing
curating
knowledge,
thus
providing
stability
future
community
curation.
The
website
been
redesigned
improve
enhance
user
experience.
This
next
generation
continues
support
existing
features
while
improving
maintainability
database
facilitating
input
by
new
functionality
leveraging
automation.
Nature Communications,
Journal Year:
2022,
Volume and Issue:
13(1)
Published: July 26, 2022
Several
common
psychiatric
and
neurodegenerative
diseases
share
epidemiologic
risk;
however,
whether
they
pathophysiology
is
unclear
the
focus
of
our
investigation.
Using
25
GWAS
results
LD
score
regression,
we
find
eight
significant
genetic
correlations
between
diseases.
We
integrate
with
human
brain
transcriptomes
(n
=
888)
proteomes
722)
to
identify
cis-
trans-
transcripts
proteins
that
are
consistent
a
pleiotropic
or
causal
role
in
each
disease,
referred
as
for
brevity.
Within
disease
group,
many
distinct
shared
proteins.
Remarkably,
30%
(13
42)
disorders.
Furthermore,
2.6-fold
more
protein-protein
interactions
among
than
expected
by
chance.
Together,
findings
suggest
these
have
molecular
pathophysiology,
which
has
important
ramifications
early
treatment
therapeutic
development.
