DeepSpaceDB
genomics.virus.kyoto-u.ac.jp/deepspacedb/

>2k #SpatialTranscriptomics Visium samples

👉Interactive, downloadable data analysis
👉Cross-sample/Cross-study comparison
👉Analyze your own data
👉Database-wide gene/pathway inquiry

#NucAcidRes 2026
academic.oup.com/nar/article/...

Group-based Prediction System (GPS) 6.0

gps.biocuckoo.cn

Online server for protein Post-Translational Modifications
Kinase-specific phosphosite prediction across 185 species!

>10 other PTMs

#NucAcidRes 2023
academic.oup.com/nar/article/...

#AlternativeSplicing

Systematic profiling of AS program & splicing factors (RBPMS, RBFOX2, MBNL1/2, Quaking) in Smooth Muscle Cell

RBPMS, RBFOX2 & MBNL1/2, but not QK, are pro-contractile in PAC1 SMC

#NucAcidRes 2025
academic.oup.com/nar/article/...

Human Ageing Genomic Resources
#Aging

A web portal for major aging research databases
GenAge
AnAge
DrugAge
CellAge
GenDR
LongevityMap

genomics.senescence.info

#NucAcidRes 2024
academic.oup.com/nar/article/...

CellMarker 2.0
An updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

117.50.127.228/CellMarker/i...

A nice resource for cell type markers for supervised clustering😁

#NucAcidRes 2023
academic.oup.com/nar/article/...

#LiquidLiquidPhaseSeparation #Heterochromatin

CK2-dependent N-term Ser11-Ser14 phosphorylation & basic segment b4 (K68-K72) of HP1α is critical for its LLPS & heterochromatin assembly

Yoshifumi Nishimura lab #NucAcidRes 2025
academic.oup.com/nar/article/...

SigCom Library of Integrated Network-based Cellular Signatures/LINCS: data & metadata search engine for a million gene expression signatures

Just fill your DEG list to explore the signatures😆

downloadable processed data L1000 GEO/CREEDS GTEx

#NucAcidRes 2022
maayanlab.cloud/sigcom-lincs...

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

Now KnockTF 2.0 👤🐭🌱🌽

>1400 transcriptomes
~800 TF/TcoF
www.licpathway.net/KnockTF/inde...

Go to "Search" for your TF
Not Quick Search

#NucAcidRes 2020
academic.oup.com/nar/article/...

CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis & modeling of aggregated data
Must-recommend😎

>1700 datasets
108+ million unique cells
>900 cell types

cellxgene.cziscience.com

@cziscience.bsky.social #NucAcidRes 2025
academic.oup.com/nar/article/...

UbiNet 2.0: Experimentally validated 3332 E3 ubiquitin ligase–substrate interactions

Not sure how updated the website is (Network module not accessible now😑), but the E3 ligase motif archive is still convenient
awi.cuhk.edu.cn/~ubinet/brow...

#NucAcidRes 2021
academic.oup.com/database/art...

#Heterochromatin Homeostasis H3K9me3 H3K27me3

H3K9me3-depleted cells (Setdb1/Suv39h1/Suv39h2/Ehmt1/Ehmt2 5KO🤠) keep their heterochromatin abundance & lamin A/C association & retrotransposon activ

Original H3K9me3 zone is Compensated by H3K27me3

#NucAcidRes 2023
academic.oup.com/nar/article/...