TF Regulatory Network Builder
Input data
cpg_transcripts.csv
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Met_5hmC cutoff (%)
Condition
Both
MS
HC
TF to gene source
DoRothEA (built in)
CoLlecTRI (decoupleR)
JASPAR 2024 (scan CpGs)
DoRothEA + CoLlecTRI
DoRothEA + CoLlecTRI + JASPAR
TRRUST v2 (upload)
Upload TF target CSV
TF target CSV
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DoRothEA confidence
A
B
C
D
E
TRRUST v2 human .txt/.tsv
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CpG window (bp, each side)
PWM cutoff (%)
JASPAR collection
CORE
VERTEBRATES
NON-REDUNDANT
INSECTS
NEMATODES
FUNGI
PLANTS
UROCHORDATES
Organism
Human (9606)
Mouse (10090)
Rat (10116)
Zebrafish (7955)
Fruit fly (7227)
Nematode (6239)
Yeast (559292)
Min CpG hits per TF gene pair
Cores for JASPAR scan
JASPAR MoR p value cutoff
Select TFs
Only 5mC enriched
ARNT2
KLF10
KLF12
KLF14
KLF6
SP1
SP2
SP4
Select all
Clear
Only 5hmC enriched
Atf1
E2F6
E2F8
HES1
NHLH1
RFX7
TFCP2
TFDP1
ZBTB7C
Select all
Clear
5mC and 5hmC enriched
Ahr::Arnt
Arnt
ARNT::HIF1A
Arntl
BHLHE40
CLOCK
Creb3l2
CREB3L4
CUX1
CUX2
EPAS1
FOSL1::JUND
GCM2
Gmeb1
GMEB2
HES2
HEY2
HIF1A
HOXA9
KLF15
KLF7
MAX
Mlxip
MLXIPL
MNT
MYC
MYCN
Npas2
OVOL2
RUNX2
SOHLH2
TCFL5
TFEB
TFEC
ZBTB17
ZFP57
Zfp961
ZNF417
Select all
Clear
Allow self loops
Output prefix
Build network
Downloads
Edges (CSV)
Nodes (CSV)
Bubble plot (PDF)
Enrichment table (CSV)
JASPAR MoR per TF (CSV)
HPA heatmap matrix (CSV)
Enrichment heatmap (PNG)
Enrichment heatmap (SVG)
Save / load network
You can save a built network (and JASPAR MoR, if available) as an RDS and load it later without rerunning JASPAR.
Save current network (RDS)
Load saved network (RDS)
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Clear loaded network
Summary
Network
Enrichment / Heatmap
HPA single nuclei brain
JASPAR inferred mode of regulation (per TF)
Wikigenes (embedded) and other sources
Viewer options
Wikigenes height (px)
Other sources
Show
GO BP
Reactome
Plot type
Heatmap
Bubble
Enrichment (union of all TF targets)
Per TF heatmap on UNION terms
Top enriched terms to include
Bubble plot (SVG)
HPA single nuclei brain .tsv
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Expected columns: Gene, Gene name, Brain region, Cluster, Cluster type, Read count, nCPM
Brain region mode
Single brain region
Mean over all brain regions
Use only genes enriched in top 50 pathways + their TFs
Use only TFs (no targets)
Download HPA heatmap (SVG)
Single gene brain region and cluster view
Download gene plot (SVG)