bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 12, 2024
Abstract
Platelets
are
vital
in
many
pathophysiological
processes,
yet
there
is
a
lack
of
comprehensive
resource
dedicated
specifically
to
platelet
research.
To
fill
this
gap,
we
have
developed
PlateletBase,
knowledge
base
aimed
at
enhancing
the
understanding
and
study
platelets
related
diseases.
Our
team
retrieved
information
from
various
public
databases,
extracting
analyzing
RNA-seq
data
3,711
samples
across
41
different
conditions
available
on
NCBI.
PlateletBase
offers
six
analytical
visualization
tools,
enabling
users
perform
gene
similarity
analysis,
pair
correlation,
multi-correlation,
expression
ranking,
clinical
association,
annotation
for
platelets.
The
current
version
includes
10,278
genomic
entries,
31,758
transcriptomic
4,869
proteomic
2,614
omics
1,833
drugs,
97
resources,
438
diseases/traits,
analysis
modules.
Each
entry
has
been
carefully
curated
supported
by
experimental
evidence.
Additionally,
features
user-friendly
interface
designed
efficient
querying,
manipulation,
browsing,
visualization,
detailed
protein
information.
Case
results,
such
as
those
gray
syndrome
angina
pectoris,
demonstrate
that
tool
can
aid
identifying
diagnostic
biomarkers
exploring
disease
mechanisms,
significantly
advancing
research
functionality
its
applications.
accessible
http://plateletbase.clinlabomics.org.cn/
.
mSystems,
Journal Year:
2024,
Volume and Issue:
9(6)
Published: May 16, 2024
A
dysfunction
of
human
host
genes
and
proteins
in
coronavirus
infectious
disease
2019
(COVID-19)
caused
by
severe
acute
respiratory
syndrome
2
(SARS-CoV-2)
is
a
key
factor
impacting
clinical
symptoms
outcomes.
Yet,
detailed
understanding
immune
responses
still
incomplete.
Here,
we
applied
RNA
sequencing
to
94
samples
COVID-19
patients
with
without
hematological
tumors
as
well
uninfected
non-tumor
individuals
obtain
comprehensive
transcriptome
landscape
both
tumor
individuals.
In
our
analysis,
further
accounted
for
the
human-SARS-CoV-2
protein
interactome,
complex
subnetworks
understand
mechanisms
SARS-CoV-2
infection
responses.
Our
data
sets
enabled
us
identify
important
(non-)targeted
differentially
expressed
complexes
post-SARS-CoV-2
We
found
several
unique
genes,
complexes,
functions/pathways
such
blood
coagulation
(APOE,
SERPINE1,
SERPINE2,
TFPI),
lipoprotein
particle
remodeling
(APOC2,
APOE,
CETP),
pro-B
cell
differentiation
(IGHM,
VPREB1,
IGLL1)
during
tumors.
particular,
gene
that
associated
remodeling,
not
only
upregulated
but
also
significantly
dead
tumors,
providing
clues
design
future
therapeutic
strategies
specifically
targeting
provide
rich
resource
specific
pathogenesis
immunocompromised
patients,
those
malignancies,
developing
effective
therapeutics
COVID-19.
iScience,
Journal Year:
2024,
Volume and Issue:
27(3), P. 109177 - 109177
Published: Feb. 8, 2024
The
COVID-19
pandemic,
driven
by
the
SARS-CoV-2
virus
and
its
variants,
highlights
important
role
of
understanding
host-viral
molecular
interactions
influencing
infection
outcomes.
Alternative
splicing
post-infection
can
impact
both
host
responses
viral
replication.
We
analyzed
RNA
patterns
in
immune
cells
across
various
considering
immunization
status.
Using
a
dataset
190
RNA-seq
samples
from
our
prior
studies,
we
observed
substantial
deactivation
alternative
splicing-related
genes
patients.
alterations
varied
significantly
depending
on
infecting
variant
history.
Notably,
Alpha
or
Beta-infected
patients
differed
controls,
while
Omicron-infected
displayed
profile
closer
to
controls.
Particularly,
vaccinated
individuals
showed
distinct
dynamic
not
widely
shared
among
other
groups.
Our
findings
underscore
intricate
interplay
between
vaccination-induced
immunity,
splicing,
emphasizing
need
for
further
investigations
deepen
guide
therapeutic
development.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Dec. 12, 2024
Abstract
Platelets
are
vital
in
many
pathophysiological
processes,
yet
there
is
a
lack
of
comprehensive
resource
dedicated
specifically
to
platelet
research.
To
fill
this
gap,
we
have
developed
PlateletBase,
knowledge
base
aimed
at
enhancing
the
understanding
and
study
platelets
related
diseases.
Our
team
retrieved
information
from
various
public
databases,
extracting
analyzing
RNA-seq
data
3,711
samples
across
41
different
conditions
available
on
NCBI.
PlateletBase
offers
six
analytical
visualization
tools,
enabling
users
perform
gene
similarity
analysis,
pair
correlation,
multi-correlation,
expression
ranking,
clinical
association,
annotation
for
platelets.
The
current
version
includes
10,278
genomic
entries,
31,758
transcriptomic
4,869
proteomic
2,614
omics
1,833
drugs,
97
resources,
438
diseases/traits,
analysis
modules.
Each
entry
has
been
carefully
curated
supported
by
experimental
evidence.
Additionally,
features
user-friendly
interface
designed
efficient
querying,
manipulation,
browsing,
visualization,
detailed
protein
information.
Case
results,
such
as
those
gray
syndrome
angina
pectoris,
demonstrate
that
tool
can
aid
identifying
diagnostic
biomarkers
exploring
disease
mechanisms,
significantly
advancing
research
functionality
its
applications.
accessible
http://plateletbase.clinlabomics.org.cn/
.
