Disease table of BARE LYMPHOCYTE SYNDROME, TYPE II OMIM ID: 209920

Gene-disease associations table

GeneAssociated with BARE LYMPHOCYTE SYNDROME, TYPE II inLink to HGNCCytogenetic bandNumber of associated diseasesAssociated diseases
CIITAOMIM, HUMSAVARHGNC link16p13.132209920, 180300
RFXANKOMIM, HUMSAVARHGNC link19p13.111209920
SMAD9ClinVarHGNC link13q13.32209920, PS178600
RFXAPClinVar, OMIMHGNC link13q13.31209920
RFX5OMIM, HUMSAVARHGNC link1q21.31209920

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Relations among genes:

Tandem repeat annotations from DGD
Cytogenetic band analysis
By sub-band
Shared sub_bandNumber of genes associated with the diseaseGenes associated with the disease
13q13.32RFXAP, SMAD9
By band
Shared bandNumber of genes associated with the diseaseGenes associated with the disease
13q132RFXAP, SMAD9
By region
Shared regionNumber of genes associated with the diseaseGenes associated with the disease
13q12RFXAP, SMAD9
By arm
Shared armNumber of genes associated with the diseaseGenes associated with the disease
13q2RFXAP, SMAD9
By chromosome
Shared chromosomeNumber of genes associated with the diseaseGenes associated with the disease
132RFXAP, SMAD9
Transcription Factors (TF) annotation from TRRUST
TFassociated to this disease# regulated genesRegulated genes# regulated genes associated with this diseaseRegulated genes associated with this disease
CIITAYES30IRF2, HDAC2, COL1A2, HLA-DRB4, HLA-DRB1, HLA-DRB3, HLA-DRA, IL4, HLA-DMA, HLA-C, SIRT1, HLA-DQB1, HLA-B, SLC26A3, HLA-A, PLXNA1, COL1A1, HLA-DMB, HLA-DRB5, S100A4, MMP9, IRF1, PSMC5, HLA-DOB, HLA-DOA, HLA-DPB1, HLA-G, RAB4B, CREBBP, FASLG0
RFXANKYES15HLA-DQA2, HLA-DQA1, HLA-DQB2, HLA-DQB1, HLA-DMA, HLA-DRB4, HLA-DOA, HLA-DPB1, HLA-DRB5, HLA-DRB1, HLA-DMB, HLA-DPA1, HLA-DRB3, HLA-DOB, HLA-DRA0
RFXAPYES15HLA-DQA2, HLA-DQA1, HLA-DQB2, HLA-DQB1, HLA-DMA, HLA-DRB4, HLA-DOA, HLA-DPB1, HLA-DRB5, HLA-DRB1, HLA-DMB, HLA-DPA1, HLA-DRB3, HLA-DOB, HLA-DRA0
RFX5YES18HLA-DQA2, HLA-DQA1, HLA-DQB2, HLA-DQB1, HLA-DMA, COL1A2, HDAC2, HLA-DRB4, IFNG, HLA-DOA, HLA-DPB1, HLA-DRB5, HLA-DRB1, HLA-DMB, HLA-DPA1, HLA-DRB3, HLA-DOB, HLA-DRA0
regulated geneassociated to this disease# TFsTFs # TFs associated with this diseaseTFs associated with this disease
CIITAYES9IRF2, PRDM1, IRF1, USF1, EZH2, STAT1, RFX1, PPARG, MYCN0
HDAC2NO4CIITA, MYC, MYCN, RFX52CIITA, RFX5
HLA-DRANO9RFXAP, RFX5, YY1, RFXANK, RFX1, CIITA, ILF3, HDAC1, POU2F24CIITA, RFXANK, RFXAP, RFX5
HLA-DQA2NO3RFXANK, RFXAP, RFX53RFXANK, RFXAP, RFX5
HLA-DQB1NO6RFXANK, RFX5, RFXAP, CREB1, CIITA, DEK4CIITA, RFXANK, RFXAP, RFX5
HLA-DQB2NO3RFXANK, RFXAP, RFX53RFXANK, RFXAP, RFX5
HLA-DPB1NO5CIITA, RFXANK, RFXAP, RFX1, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DRB3NO4CIITA, RFXANK, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DRB1NO5CIITA, RFXANK, ILF3, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DRB4NO4CIITA, RFXANK, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DRB5NO4CIITA, RFXANK, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
COL1A2NO9RFX5, STAT6, YY1, CEBPZ, MYB, RELA, CIITA, NFKB1, SIRT12CIITA, RFX5
HLA-DOANO4CIITA, RFXANK, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DOBNO6RFXANK, RFX5, RFXAP, CREB1, CIITA, POU2F24CIITA, RFXANK, RFXAP, RFX5
HLA-DPA1NO3RFXANK, RFXAP, RFX53RFXANK, RFXAP, RFX5
HLA-DMBNO5CIITA, RFXANK, RFXAP, RFX1, RFX54CIITA, RFXANK, RFXAP, RFX5
HLA-DQA1NO4RFXANK, ILF3, RFXAP, RFX53RFXANK, RFXAP, RFX5
HLA-DMANO4CIITA, RFXANK, RFXAP, RFX54CIITA, RFXANK, RFXAP, RFX5
Interactions from BIOGRID - physical
Gene1Gene2Direct InteractionNumber of shared interactorsShared genes in interaction
CIITARFXANKYes4HDAC4, RFXANK, HDAC5, RFX5
CIITARFXAPNo3HDAC4, RFXANK, RFX5
CIITARFX5Yes4HDAC4, HDAC2, RFXANK, PPARG
RFXANKRFXAPYes3HDAC4, RFXANK, RFX5
RFXANKRFX5Yes6RFXANK, RFXAP, CIITA, HDAC4, NXF1, MOV10
RFXAPRFX5Yes4HDAC4, RFXANK, MLLT1, ANKRA2

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic
Interactions from STRING
Interactions from CORUM
Interactions from CENSUS
Interactions from PDB
Gene1Gene2InteractionNumber of common interactorsCommon genes in interaction
RFXANKRFXAPNo1RFX5
RFXANKRFX5Yes2RFXANK, RFX5
RFXAPRFX5Yes2RFXAP, RFX5

Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from manually curated literature
KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

KEGG termKEGG term IDICNumber of genes with the same termGenes
Primary immunodeficiencyhsa053407.524CIITA, RFXANK, RFXAP, RFX5
Tuberculosishsa051525.174CIITA, RFXANK, RFXAP, RFX5
Antigen processing and presentationhsa046126.044CIITA, RFXANK, RFXAP, RFX5

NET-GE enrichment

Term New enriched termICP valueGenes
Immune diseasesNEW4.470.0CIITA, RFXANK, RFXAP, RFX5
Infectious diseases: BacterialNEW3.760.003CIITA, RFXANK, RFXAP, RFX5
Antigen processing and presentation (hsa04612) -6.040.0CIITA, RFXANK, RFXAP, RFX5
Immune systemNEW2.920.026CIITA, RFXANK, RFXAP, RFX5
Tuberculosis (hsa05152) -5.170.0CIITA, RFXANK, RFXAP, RFX5
Primary immunodeficiency (hsa05340) -7.520.0CIITA, RFXANK, RFXAP, RFX5
REACTOME pathways annotation: shared terms / NET-GE enrichment (no shared terms)
GO - molecular function annotation: shared terms / NET-GE enrichment

Shared terms

GOICNumber of genes with the same GOGenes
binding (GO:0005488) 0.185CIITA, SMAD9, RFXANK, RFXAP, RFX5
organic cyclic compound binding (GO:0097159) 1.055CIITA, SMAD9, RFXANK, RFXAP, RFX5
heterocyclic compound binding (GO:1901363) 1.065SMAD9, CIITA, RFXANK, RFXAP, RFX5
nucleic acid binding (GO:0003676) 1.445CIITA, SMAD9, RFXANK, RFXAP, RFX5
DNA binding (GO:0003677) 1.925SMAD9, CIITA, RFXANK, RFXAP, RFX5
transcription factor activity, sequence-specific DNA binding (GO:0003700) 2.654SMAD9, RFXANK, RFXAP, RFX5
nucleic acid binding transcription factor activity (GO:0001071) 2.654SMAD9, RFXANK, RFXAP, RFX5
protein binding (GO:0005515) 0.464CIITA, SMAD9, RFXANK, RFX5
transcription cofactor activity (GO:0003712) 3.443CIITA, RFXANK, RFXAP
transcription factor activity, transcription factor binding (GO:0000989) 3.363CIITA, RFXANK, RFXAP
transcription factor activity, protein binding (GO:0000988) 3.353CIITA, RFXANK, RFXAP
regulatory region nucleic acid binding (GO:0001067) 3.032CIITA, RFX5
transcription regulatory region DNA binding (GO:0044212) 3.032CIITA, RFX5
transcription coactivator activity (GO:0003713) 4.042CIITA, RFXAP
regulatory region DNA binding (GO:0000975) 3.032CIITA, RFX5

NET-GE enrichment

Term New enriched termICP valueGenes
nucleic acid binding (GO:0003676) -1.440.04SMAD9, CIITA, RFXANK, RFXAP, RFX5
sequence-specific DNA binding transcription factor activity (GO:0003700) -2.650.004SMAD9, CIITA, RFXANK, RFXAP, RFX5
protein binding transcription factor activity (GO:0000988) -3.350.014CIITA, RFXANK, RFXAP
transcription cofactor activity (GO:0003712) -3.440.011CIITA, RFXANK, RFXAP
nucleic acid binding transcription factor activity (GO:0001071) -2.650.009CIITA, SMAD9, RFXANK, RFXAP, RFX5
transcription factor binding transcription factor activity (GO:0000989) -3.360.014CIITA, RFXANK, RFXAP
DNA binding (GO:0003677) -1.920.003SMAD9, CIITA, RFXANK, RFXAP, RFX5
GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

GOICNumber of genes with the same GOGenes
regulation of nucleobase-containing compound metabolic process (GO:0019219) 1.435SMAD9, CIITA, RFXANK, RFXAP, RFX5
regulation of primary metabolic process (GO:0080090) 1.085CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of metabolic process (GO:0019222) 1.025CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of macromolecule metabolic process (GO:0060255) 1.085CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of cellular biosynthetic process (GO:0031326) 1.385CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of cellular metabolic process (GO:0031323) 1.075CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of RNA metabolic process (GO:0051252) 1.525SMAD9, CIITA, RFXANK, RFXAP, RFX5
regulation of biosynthetic process (GO:0009889) 1.375CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of nucleic acid-templated transcription (GO:1903506) 1.555CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of cellular process (GO:0050794) 0.55CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of transcription, DNA-templated (GO:0006355) 1.565CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of macromolecule biosynthetic process (GO:0010556) 1.435SMAD9, CIITA, RFXANK, RFXAP, RFX5
biological regulation (GO:0065007) 0.395CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of nitrogen compound metabolic process (GO:0051171) 1.365SMAD9, CIITA, RFXANK, RFXAP, RFX5
regulation of RNA biosynthetic process (GO:2001141) 1.555CIITA, SMAD9, RFXANK, RFXAP, RFX5
regulation of gene expression (GO:0010468) 1.375SMAD9, CIITA, RFXANK, RFXAP, RFX5
regulation of cellular macromolecule biosynthetic process (GO:2000112) 1.465SMAD9, CIITA, RFXANK, RFXAP, RFX5
regulation of biological process (GO:0050789) 0.455SMAD9, CIITA, RFXANK, RFXAP, RFX5
RNA biosynthetic process (GO:0032774) 1.844CIITA, SMAD9, RFXANK, RFX5
nucleic acid metabolic process (GO:0090304) 1.464CIITA, SMAD9, RFXANK, RFX5
cellular biosynthetic process (GO:0044249) 1.374SMAD9, CIITA, RFXANK, RFX5
cellular nitrogen compound metabolic process (GO:0034641) 1.224CIITA, SMAD9, RFXANK, RFX5
nitrogen compound metabolic process (GO:0006807) 1.134SMAD9, CIITA, RFXANK, RFX5
cellular macromolecule biosynthetic process (GO:0034645) 1.664CIITA, SMAD9, RFXANK, RFX5
organic cyclic compound biosynthetic process (GO:1901362) 1.664CIITA, SMAD9, RFXANK, RFX5
nucleic acid-templated transcription (GO:0097659) 1.914CIITA, SMAD9, RFXANK, RFX5
organic substance biosynthetic process (GO:1901576) 1.344CIITA, SMAD9, RFXANK, RFX5
cellular macromolecule metabolic process (GO:0044260) 0.934CIITA, SMAD9, RFXANK, RFX5
organic substance metabolic process (GO:0071704) 0.634SMAD9, CIITA, RFXANK, RFX5
organic cyclic compound metabolic process (GO:1901360) 1.264CIITA, SMAD9, RFXANK, RFX5
heterocycle biosynthetic process (GO:0018130) 1.74SMAD9, CIITA, RFXANK, RFX5
nucleobase-containing compound metabolic process (GO:0006139) 1.354SMAD9, CIITA, RFXANK, RFX5
cellular process (GO:0009987) 0.264SMAD9, CIITA, RFXANK, RFX5
cellular aromatic compound metabolic process (GO:0006725) 1.34CIITA, SMAD9, RFXANK, RFX5
biosynthetic process (GO:0009058) 1.324SMAD9, CIITA, RFXANK, RFX5
macromolecule biosynthetic process (GO:0009059) 1.614CIITA, SMAD9, RFXANK, RFX5
metabolic process (GO:0008152) 0.584CIITA, SMAD9, RFXANK, RFX5
nucleobase-containing compound biosynthetic process (GO:0034654) 1.724CIITA, SMAD9, RFXANK, RFX5
heterocycle metabolic process (GO:0046483) 1.314SMAD9, CIITA, RFXANK, RFX5
RNA metabolic process (GO:0016070) 1.594SMAD9, CIITA, RFXANK, RFX5
primary metabolic process (GO:0044238) 0.694CIITA, SMAD9, RFXANK, RFX5
cellular nitrogen compound biosynthetic process (GO:0044271) 1.594CIITA, SMAD9, RFXANK, RFX5
cellular metabolic process (GO:0044237) 0.694CIITA, SMAD9, RFXANK, RFX5
macromolecule metabolic process (GO:0043170) 0.834SMAD9, CIITA, RFXANK, RFX5
regulation of transcription from RNA polymerase II promoter (GO:0006357) 2.244CIITA, SMAD9, RFXANK, RFX5
transcription, DNA-templated (GO:0006351) 1.914SMAD9, CIITA, RFXANK, RFX5
aromatic compound biosynthetic process (GO:0019438) 1.74SMAD9, CIITA, RFXANK, RFX5
positive regulation of nucleic acid-templated transcription (GO:1903508) 2.563CIITA, SMAD9, RFXANK
positive regulation of nucleobase-containing compound metabolic process (GO:0045935) 2.353CIITA, SMAD9, RFXANK
positive regulation of metabolic process (GO:0009893) 1.743CIITA, SMAD9, RFXANK
positive regulation of biosynthetic process (GO:0009891) 2.293CIITA, SMAD9, RFXANK
positive regulation of cellular metabolic process (GO:0031325) 1.813CIITA, SMAD9, RFXANK
positive regulation of cellular biosynthetic process (GO:0031328) 2.33CIITA, SMAD9, RFXANK
positive regulation of RNA metabolic process (GO:0051254) 2.513CIITA, SMAD9, RFXANK
positive regulation of RNA biosynthetic process (GO:1902680) 2.543CIITA, SMAD9, RFXANK
positive regulation of macromolecule biosynthetic process (GO:0010557) 2.393CIITA, SMAD9, RFXANK
positive regulation of gene expression (GO:0010628) 2.353CIITA, SMAD9, RFXANK
positive regulation of transcription from RNA polymerase II promoter (GO:0045944) 2.813CIITA, SMAD9, RFXANK
signal transduction (GO:0007165) 1.283CIITA, SMAD9, RFXANK
positive regulation of transcription, DNA-templated (GO:0045893) 2.563CIITA, SMAD9, RFXANK
positive regulation of nitrogen compound metabolic process (GO:0051173) 2.293CIITA, SMAD9, RFXANK
positive regulation of biological process (GO:0048518) 1.23CIITA, SMAD9, RFXANK
positive regulation of cellular process (GO:0048522) 1.33CIITA, SMAD9, RFXANK
positive regulation of macromolecule metabolic process (GO:0010604) 1.813CIITA, SMAD9, RFXANK
negative regulation of metabolic process (GO:0009892) 1.932CIITA, RFX5
cell surface receptor signaling pathway (GO:0007166) 2.092CIITA, SMAD9
negative regulation of biosynthetic process (GO:0009890) 2.472CIITA, RFX5
negative regulation of cellular biosynthetic process (GO:0031327) 2.492CIITA, RFX5
phosphorylation (GO:0016310) 2.632CIITA, SMAD9
negative regulation of cellular metabolic process (GO:0031324) 2.012CIITA, RFX5
negative regulation of gene expression (GO:0010629) 2.482CIITA, RFX5
cellular response to chemical stimulus (GO:0070887) 2.572CIITA, SMAD9
response to organic cyclic compound (GO:0014070) 3.072CIITA, SMAD9
cellular response to stimulus (GO:0051716) 1.972CIITA, SMAD9
negative regulation of macromolecule metabolic process (GO:0010605) 2.012CIITA, RFX5
negative regulation of transcription from RNA polymerase II promoter (GO:0000122) 3.122CIITA, RFX5
negative regulation of cellular macromolecule biosynthetic process (GO:2000113) 2.62CIITA, RFX5
response to organic substance (GO:0010033) 2.22CIITA, SMAD9
cellular response to organic substance (GO:0071310) 2.782CIITA, SMAD9
single-organism process (GO:0044699) 0.482CIITA, SMAD9
negative regulation of biological process (GO:0048519) 1.332CIITA, RFX5
developmental process (GO:0032502) 1.362CIITA, SMAD9
negative regulation of nucleobase-containing compound metabolic process (GO:0045934) 2.552CIITA, RFX5
negative regulation of nucleic acid-templated transcription (GO:1903507) 2.712CIITA, RFX5
single-organism developmental process (GO:0044767) 1.492CIITA, SMAD9
negative regulation of transcription, DNA-templated (GO:0045892) 2.752CIITA, RFX5
negative regulation of nitrogen compound metabolic process (GO:0051172) 2.472CIITA, RFX5
response to chemical (GO:0042221) 1.982CIITA, SMAD9
negative regulation of RNA metabolic process (GO:0051253) 2.662CIITA, RFX5
negative regulation of RNA biosynthetic process (GO:1902679) 2.72CIITA, RFX5
cellular response to organic cyclic compound (GO:0071407) 3.932CIITA, SMAD9
response to stimulus (GO:0050896) 1.222CIITA, SMAD9
phosphate-containing compound metabolic process (GO:0006796) 2.162CIITA, SMAD9
phosphorus metabolic process (GO:0006793) 2.152CIITA, SMAD9
negative regulation of macromolecule biosynthetic process (GO:0010558) 2.532CIITA, RFX5
negative regulation of cellular process (GO:0048523) 1.412CIITA, RFX5

NET-GE enrichment

Term New enriched termICP valueGenes
positive regulation of nucleobase-containing compound metabolic process (GO:0045935) -2.350.026CIITA, SMAD9, RFXANK, RFXAP
positive regulation of cellular biosynthetic process (GO:0031328) -2.30.033CIITA, SMAD9, RFXANK, RFXAP
regulation of transcription from RNA polymerase II promoter (GO:0006357) -2.240.036SMAD9, CIITA, RFXANK, RFX5
regulation of RNA biosynthetic process (GO:2001141) -1.550.045SMAD9, CIITA, RFXANK, RFXAP, RFX5
positive regulation of RNA metabolic process (GO:0051254) -2.510.016CIITA, SMAD9, RFXANK, RFXAP
regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664) NEW6.730.018CIITA, RFXANK
positive regulation of RNA biosynthetic process (GO:1902680) -2.540.015CIITA, SMAD9, RFXANK, RFXAP
regulation of transcription, DNA-templated (GO:0006355) -1.560.042SMAD9, CIITA, RFXANK, RFXAP, RFX5
positive regulation of macromolecule biosynthetic process (GO:0010557) -2.390.025CIITA, SMAD9, RFXANK, RFXAP
positive regulation of gene expression (GO:0010628) -2.350.019CIITA, SMAD9, RFXANK, RFXAP
positive regulation of transcription, DNA-templated (GO:0045893) -2.560.013CIITA, SMAD9, RFXANK, RFXAP
positive regulation of nitrogen compound metabolic process (GO:0051173) -2.290.028CIITA, SMAD9, RFXANK, RFXAP
positive regulation of biosynthetic process (GO:0009891) -2.290.034CIITA, SMAD9, RFXANK, RFXAP
GO - cellular component annotation: shared terms (no NET-GE enrichment)

Shared terms

GOICNumber of genes with the same GOGenes
intracellular membrane-bounded organelle (GO:0043231) 0.65SMAD9, CIITA, RFXANK, RFXAP, RFX5
nucleus (GO:0005634) 1.075CIITA, SMAD9, RFXANK, RFXAP, RFX5
cell part (GO:0044464) 0.115SMAD9, CIITA, RFXANK, RFXAP, RFX5
intracellular organelle (GO:0043229) 0.515CIITA, SMAD9, RFXANK, RFXAP, RFX5
intracellular part (GO:0044424) 0.285SMAD9, CIITA, RFXANK, RFXAP, RFX5
membrane-bounded organelle (GO:0043227) 0.475SMAD9, CIITA, RFXANK, RFXAP, RFX5
organelle (GO:0043226) 0.45SMAD9, CIITA, RFXANK, RFXAP, RFX5
nucleoplasm (GO:0005654) 1.893CIITA, SMAD9, RFXANK
intracellular organelle part (GO:0044446) 0.813CIITA, SMAD9, RFXANK
nuclear part (GO:0044428) 1.553CIITA, SMAD9, RFXANK
organelle part (GO:0044422) 0.793CIITA, SMAD9, RFXANK
cytoplasm (GO:0005737) 1.012SMAD9, RFXANK