The NFIRegulome project in PAZAR Help

Description


The NFIRegulomeDB is a database of genes regulated by the Nuclear Factor I transcription factor family compiled by the Gronostajski Lab. The long-term goal is to provide a generic annotation and search system that individual labs focussed on specific transcription factors or transcription factor families can use to keep databases on genes that their factors regulate. Eventually we'd like to link these individual databases into a distributed RegulomeDB for all known regulated genes and their associated transcription factors.
http://nfiregulome.ccr.buffalo.edu

Statistics

Regulated genes (or markers): 29
Regulatory sequences (genomic): 116
Regulatory sequences (artificial): 0
Transcription factors: 38
Transcription factor profiles: 0
Annotated publications: 30

Generate GFF

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Pre-generated GFF files are available in the downloads section. Public projects are checked weekly and updated files are generated if there are changes.

Access project data

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Homo sapiens
Mus musculus
Rattus norvegicus
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chromosome
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Restrict to one or more regulated genes or markers »
adenosine deaminase ENSG00000196839
Alpha-fetoprotein ENSRNOG00000002889
chemokine ligand 2 ENSG00000108691
cyclin-dependent kinase inhibitor 1A ENSG00000124762
cytochrome P450, family 17, subfamily A, polypeptide 1 ENSG00000148795
cytotoxic T-lymphocyte-associated protein 4 ENSG00000163599
Glial fibrillary acidic protein ENSRNOG00000002919
glial fibrillary acidic protein ENSG00000131095
Kruppel-like factor 5 ENSRNOG00000008785
lactalbumin, alpha- ENSG00000167531
lactate dehydrogenase C ENSMUSG00000030851
metallothionein 1 ENSMUSG00000031765
myelin basic protein ENSMUSG00000041607
Myelin proteolipid protein ENSRNOG00000002419
neurofilament, light polypeptide ENSMUSG00000022055
paired-like homeodomain transcription factor 2 ENSMUSG00000028023
proenkephalin ENSG00000181195
Protein-lysine 6-oxidase ENSRNOG00000014426
renin 1 structural ENSMUSG00000070645
S100 calcium binding protein B ENSG00000160307
secretoglobin, family 2A, member 1 ENSG00000124939
serpin peptidase inhibitor, clade A , member 3 ENSG00000196136
serpin peptidase inhibitor, clade E , member 1 ENSG00000106366
solute carrier family 25 , member 5 ENSG00000005022
transcription factor AP-2 alpha ENSG00000137203
transcription factor AP-2, alpha ENSMUSG00000021359
transformation related protein 53 ENSMUSG00000059552
tumor protein p53 ENSG00000141510
Whey acidic protein ENSRNOG00000008097
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Only show results with a sequence length that is bases
Restrict to one or more regulating factors »
CDX1_HUMAN ENST00000231656
CREB1_MOUSE ENSMUST00000027097
FOS_HUMAN ENST00000303562
FOS_MOUSE ENSMUST00000021674
GATA4_HUMAN ENST00000335135
GATA6_HUMAN ENST00000269216
IPF1_HUMAN ENST00000381033
LEF1_MOUSE ENSMUST00000098611
MAF_HUMAN ENST00000326043
MTF1_MOUSE ENSMUST00000030723
NFIA_HUMAN ENST00000371191
NFIA_MOUSE ENSMUST00000107055
NFIC_HUMAN ENST00000443272
NFIC_MOUSE ENSMUST00000105319
NFKB1_HUMAN ENST00000226574
NFYA_HUMAN ENST00000341376
NFYA_MOUSE ENSMUST00000078800
POU2F1_HUMAN ENST00000367866
POU2F1_MOUSE ENSMUST00000111429
RARA_MOUSE ENSMUST00000107475
RUNX2_RAT ENSRNOT00000061014
SF1_HUMAN ENST00000377390
SP1_HUMAN ENST00000317060
SP1_MOUSE ENSMUST00000001326
SP3_HUMAN ENST00000416195
SP3_MOUSE ENSMUST00000102689
STAT1_MOUSE ENSMUST00000087717
STAT5_RAT ENSRNOT00000026662
TBP_HUMAN ENST00000421512
TFAP2A_HUMAN ENST00000319516
TFAP2A_MOUSE ENSMUST00000021787
TFAP4_HUMAN ENST00000204517
YY1_HUMAN ENST00000262238
Restrict to a specific TF classification class or family »
There are no class or family annotations to filter in this project.
Restrict to protein-DNA interaction quality »
Restrict to sequences where interaction is
Restrict to expression outcome »
Restrict to sequences where expression is
Restrict to one or more evidence types »
ADMC
curated
predicted
Restrict to one or more experimental methods »
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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