The HNF4 project in PAZAR Help

Description

The HNF4 project houses data from the Sladek lab at UC Riverside (http://www.sladeklab.ucr.edu/). The project includes 107 expert curated TFBS that were bulk-uploaded with the interacting transcription factor labeled as human HNF4A. Consult each original publication to determine the actual species source of TF used in the experiments. H4 numbers assigned to regulatory sequences refer to specific binding sites.

Statistics

Regulated genes (or markers): 79
Regulatory sequences (genomic): 107
Regulatory sequences (artificial): 0
Transcription factors: 1
Transcription factor profiles: 0
Annotated publications: 70

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Access project data

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Homo sapiens
Mus musculus
Rattus norvegicus
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chromosome
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7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase ENSRNOG00000019481
acyl-CoA dehydrogenase, C-4 to C-12 straight chain ENSG00000117054
aldehyde dehydrogenase 2 family ENSG00000111275
aldo-keto reductase family 1, member C4 ENSG00000198610
aldolase B, fructose-bisphosphate ENSMUSG00000028307
alpha-1-microglobulin/bikunin precursor ENSG00000106927
alpha-fetoprotein ENSG00000081051
amino carboxymuconate semialdehyde decarboxylase ENSMUSG00000026348
angiotensinogen ENSG00000135744
apolipoprotein A-I ENSG00000118137
apolipoprotein A-II ENSG00000158874
apolipoprotein A-IV ENSG00000110244
apolipoprotein A-V ENSG00000110243
apolipoprotein B ENSG00000084674
apolipoprotein C-II ENSMUSG00000002992
apolipoprotein C-II ENSG00000234906
apolipoprotein C-III ENSG00000110245
aquaporin 4 ENSMUSG00000024411
bile acid-Coenzyme A: amino acid N-acyltransferase ENSMUSG00000039653
cadherin 1 ENSMUSG00000000303
cadherin-related family member 5 ENSMUSG00000025497
carboxylesterase 2C ENSMUSG00000061825
coagulation factor II ENSG00000180210
coagulation factor IX ENSG00000101981
coagulation factor VII ENSMUSG00000031443
coagulation factor VII ENSG00000057593
coagulation factor X ENSG00000126218
coxsackie virus and adenovirus receptor ENSMUSG00000022865
crumbs homolog 3 ENSMUSG00000044279
Cytochrome P450 3A1 ENSRNOG00000032560
Cytochrome P450 4A10 ENSRNOG00000009597
cytochrome P450, family 2, subfamily a, polypeptide 4 ENSMUSG00000074254
cytochrome P450, family 2, subfamily C, polypeptide 9 ENSG00000138109
cytochrome P450, family 2, subfamily D, polypeptide 6 ENSG00000100197
cytochrome P450, family 3, subfamily a, polypeptide 16 ENSMUSG00000038656
cytochrome P450, family 3, subfamily A, polypeptide 4 ENSG00000160868
cytochrome P450, family 7, subfamily A, polypeptide 1 ENSG00000167910
cytochrome P450, family 8, subfamily B, polypeptide 1 ENSG00000180432
Fatty acid-binding protein, intestinal ENSRNOG00000024947
flavin containing monooxygenase 1 ENSG00000010932
gap junction protein, beta 1 ENSMUSG00000047797
Glucokinase ENSRNOG00000014447
glucose-6-phosphatase, catalytic subunit ENSG00000131482
glycine amidinotransferase ENSMUSG00000027199
glycosylphosphatidylinositol specific phospholipase D1 ENSMUSG00000021340
guanylate cyclase 2C ENSG00000070019
hepatic nuclear factor 4, alpha ENSMUSG00000017950
Hepatocyte nuclear factor 6 ENSRNOG00000008095
HNF1 homeobox A ENSG00000135100
HNF1 homeobox B ENSMUSG00000020679
Insulin-1Insulin-1 B chainInsulin-1 A chain ENSRNOG00000012052
lectin, galactose binding, soluble 9 ENSMUSG00000001123
macrophage stimulating 1 ENSG00000173531
microsomal triglyceride transfer protein ENSG00000138823
nephronectin ENSMUSG00000040998
neuraminidase 3 ENSMUSG00000035239
nuclear receptor subfamily 0, group B, member 2 ENSG00000131910
nuclear receptor subfamily 1, group I, member 3 ENSMUSG00000005677
Ornithine carbamoyltransferase, mitochondrial ENSRNOG00000003370
p21 protein -activated kinase 7 ENSG00000101349
peroxisome proliferator-activated receptor alpha ENSG00000186951
Phosphoenolpyruvate carboxykinase, cytosolic ENSRNOG00000028616
plakophilin 2 ENSMUSG00000041957
potassium inwardly rectifying channel, subfamily J, member 11 ENSMUSG00000070561
proline dehydrogenase 2 ENSMUSG00000036892
Pyruvate kinase isozymes R/L ENSRNOG00000020420
Retinol-binding protein 2 ENSRNOG00000013932
ribosomal protein S6 kinase, 90kDa, polypeptide 6 ENSG00000072133
serpin peptidase inhibitor, clade C , member 1 ENSG00000117601
serum amyloid A 1 ENSMUSG00000074115
sex hormone-binding globulin ENSG00000129214
solute carrier family 22 , member 1 ENSG00000175003
solute carrier family 27 , member 5 ENSMUSG00000030382
solute carrier family 39 , member 4 ENSMUSG00000063354
transferrin ENSMUSG00000032554
transthyretin ENSMUSG00000061808
Tyrosine aminotransferase ENSRNOG00000016348
vitronectin ENSMUSG00000017344
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ADMC
curated
predicted
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15688014
COMPILED
COMPUTATIONAL PREDICTION
DNASE I FOOTPRINTING
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::DIRECT GEL SHIFT
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::DIRECT GEL SHIFT WITH WESTERN BLOT DETECTION
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::GEL SHIFT COMPETITION
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::SUPERSHIFT
ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA)::UNKNOWN
EMSA
EXPERT CURATED::LITERATURE DERIVED
GENE CO-EXPRESSION::CO-EXPRESSED GENES DETERMINED THROUGH REPORTER GENE EXPERIMENTS
IN-VIVO HUMAN CD4 ASSAY
MUTAGENESIS::EXONUCLEASE DIGESTION
MUTAGENESIS::EXONUCLEASE III DIGESTION
MUTAGENESIS::OLIGONUCLEOTIDE SYNTHESIS
MUTAGENESIS::PCR
MUTAGENESIS::RESTRICTION ENDONUCLEASE DIGESTION
MUTAGENESIS::SITE-DIRECTED
MUTAGENESIS::UNKNOWN
N/A
NA
PROTEIN BINDING ASSAY :: CHROMATIN IMMUNOPRECIPITATION WITH TAG SEQUENCING (CHIP-TS)
PROTEIN BINDING ASSAY::CHROMATIN IMMUNOPRECIPITATION (CHIP)
PROTEIN BINDING ASSAY::CHROMATIN IMMUNOPRECIPITATION WITH TAG SEQUENCING (CHIP-TS)
PROTEIN BINDING ASSAY::DNA-PROTEIN PRECIPITATION ASSAY
PROTEIN BINDING ASSAY::DNA-PROTEIN PRECIPITATION ASSAY WITH ELISA DETECTION
PROTEIN BINDING ASSAY::DNASE FOOTPRINTING ASSAY
PROTEIN BINDING ASSAY::DNASE FOOTPRINTING COMPETITION ASSAY
PROTEIN BINDING ASSAY::IN-VIVO FOOTPRINTING ASSAY
PROTEIN BINDING ASSAY::METHYLATION INTERFERENCE
PROTEIN BINDING ASSAY::METHYLATION INTERFERENCE ASSAY
PROTEIN BINDING ASSAY::UNKNOWN
PROTEIN BINDING ASSAY::WESTERN BLOT ASSAY
PROTEIN BINDING ASSAY::YEAST 1-HYBRID ASSAY
PROTEIN EXPRESSION ASSAY::ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA)
PROTEIN EXPRESSION ASSAY::INDIRECT IMMUNOFLUORESCENCE
PROTEIN EXPRESSION ASSAY::LUCIFERASE EXPRESSION ASSAY
PROTEIN EXPRESSION ASSAY::WESTERN BLOT ASSAY
REPORTER GENE ASSAY
REPORTER GENE ASSAY:: TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY
REPORTER GENE ASSAY:: TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY WITH ELISA DETECTION
REPORTER GENE ASSAY::BETA-GLOBIN EXPRESSION ASSAY
REPORTER GENE ASSAY::CHLORAMPHENICOL ACETYLTRANSFERASE (CAT) ASSAY
REPORTER GENE ASSAY::DUAL LUCIFERASE REPORTER GENE ASSAY
REPORTER GENE ASSAY::IN-VITRO VIRUS REPLICATION ASSAY
REPORTER GENE ASSAY::IN-VIVO CHLORAMPHENICOL ACETYLTRANSFERASE (CAT) ASSAY
REPORTER GENE ASSAY::IN-VIVO GENE EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO GFP EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO LACZ EXPRESSION ASSAY
REPORTER GENE ASSAY::IN-VIVO LUCIFERASE EXPRESSION ASSAY
REPORTER GENE ASSAY::RABBIT BETA-GLOBIN EXPRESSION ASSAY
REPORTER GENE ASSAY::SECRETED ALKALINE PHOSPHATASE (SEAP) ASSAY
REPORTER GENE ASSAY::SITE-SPECIFIC STABLE TRANSFECTION GFP ASSAY BY CRE-LOX RECOMBINATION
REPORTER GENE ASSAY::STABLE TRANSFECTION CAT ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION DSRED ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION LACZ ASSAY
REPORTER GENE ASSAY::STABLE TRANSFECTION LUCIFERASE ASSAY
REPORTER GENE ASSAY::STABLY INCORPORATED GFP TRANSGENE ASSAY
REPORTER GENE ASSAY::TARGETED IN-VIVO EXPRESSION ASSAY BY IN UTERO ELECTROPORATION
REPORTER GENE ASSAY::TARGETED IN-VIVO GENE EXPRESSION ASSAY BY NON-VIRAL INJECTION
REPORTER GENE ASSAY::TARGETED IN-VIVO GFP EXPRESSION ASSAY BY VIRAL INJECTION
REPORTER GENE ASSAY::TARGETED IN-VIVO LACZ EXPRESSION ASSAY BY VIRAL INJECTION
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION GENE EXPRESSION ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION GFP ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION HUMAN GROWTH HORMONE ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION LACZ ASSAY
REPORTER GENE ASSAY::TRANSIENT TRANSFECTION LUCIFERASE ASSAY
REPORTER GENE ASSAY::UNKNOWN
REPORTER GENE ASSAY::VIRAL INFECTION LUCIFERASE ASSAY
RNA EXPRESSION ASSAY::IN-VITRO TRANSCRIPTION ASSAY WITH DETECTION BY PRIMER EXTENSION
RNA EXPRESSION ASSAY::NORTHERN BLOT
RNA EXPRESSION ASSAY::PRIMER EXTENSION ANALYSIS WITH POLY(A)+ RNA
RNA EXPRESSION ASSAY::REAL TIME PCR
RNA EXPRESSION ASSAY::REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION (RT-PCR)
RNA EXPRESSION ASSAY::RNASE PROTECTION ASSAY (RPA)
RNA EXPRESSION ASSAY::WHOLE-MOUNT IN SITU HYBRIDIZATION
RNA STABILITY ASSAY::RNA SYNTHESIS BLOCKING
SELEX
SEQUENCE CONSERVATION::CO-EXPRESSED GENE CONSERVATION
SEQUENCE CONSERVATION::CONSERVATION FOUND BY ALIGNMENT
SEQUENCE CONSERVATION::ORTHOLOGOUS GENE CONSERVATION
SITE-DIRECTED MUTAGENESIS
UNKNOWN::CHROMATIN IMMUNOPRECIPITATION (CHIP)
UNKNOWN::UNKNOWN
YEAST ONE-HYBRID
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