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Gene: IRF4 |
Gene summary for IRF4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | IRF4 | Gene ID | 3662 |
| Gene name | interferon regulatory factor 4 | |
| Gene Alias | LSIRF | |
| Cytomap | 6p25.3 | |
| Gene Type | protein-coding | GO ID | GO:0001562 | UniProtAcc | Q15306 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 3662 | IRF4 | C09 | Human | Oral cavity | OSCC | 1.84e-36 | 1.09e+00 | 0.1431 |
| 3662 | IRF4 | EOLP-1 | Human | Oral cavity | EOLP | 4.63e-17 | 5.16e-01 | -0.0202 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000647321 | Oral cavity | EOLP | protein acetylation | 44/2218 | 201/18723 | 3.69e-05 | 5.12e-04 | 44 |
| GO:00022633 | Oral cavity | EOLP | cell activation involved in immune response | 56/2218 | 279/18723 | 4.91e-05 | 6.47e-04 | 56 |
| GO:00023662 | Oral cavity | EOLP | leukocyte activation involved in immune response | 55/2218 | 275/18723 | 6.32e-05 | 7.90e-04 | 55 |
| GO:00022852 | Oral cavity | EOLP | lymphocyte activation involved in immune response | 42/2218 | 194/18723 | 7.17e-05 | 8.82e-04 | 42 |
| GO:0046637 | Oral cavity | EOLP | regulation of alpha-beta T cell differentiation | 20/2218 | 68/18723 | 7.88e-05 | 9.51e-04 | 20 |
| GO:001839421 | Oral cavity | EOLP | peptidyl-lysine acetylation | 37/2218 | 169/18723 | 1.48e-04 | 1.58e-03 | 37 |
| GO:0043370 | Oral cavity | EOLP | regulation of CD4-positive, alpha-beta T cell differentiation | 16/2218 | 51/18723 | 1.75e-04 | 1.80e-03 | 16 |
| GO:00455803 | Oral cavity | EOLP | regulation of T cell differentiation | 33/2218 | 146/18723 | 1.75e-04 | 1.81e-03 | 33 |
| GO:001839321 | Oral cavity | EOLP | internal peptidyl-lysine acetylation | 34/2218 | 158/18723 | 3.76e-04 | 3.40e-03 | 34 |
| GO:001657321 | Oral cavity | EOLP | histone acetylation | 33/2218 | 152/18723 | 3.85e-04 | 3.46e-03 | 33 |
| GO:000647521 | Oral cavity | EOLP | internal protein amino acid acetylation | 34/2218 | 160/18723 | 4.79e-04 | 4.19e-03 | 34 |
| GO:0042093 | Oral cavity | EOLP | T-helper cell differentiation | 18/2218 | 66/18723 | 4.94e-04 | 4.31e-03 | 18 |
| GO:00026974 | Oral cavity | EOLP | regulation of immune effector process | 61/2218 | 339/18723 | 5.48e-04 | 4.68e-03 | 61 |
| GO:00439672 | Oral cavity | EOLP | histone H4 acetylation | 18/2218 | 67/18723 | 6.02e-04 | 5.04e-03 | 18 |
| GO:00022864 | Oral cavity | EOLP | T cell activation involved in immune response | 26/2218 | 114/18723 | 7.06e-04 | 5.78e-03 | 26 |
| GO:0002294 | Oral cavity | EOLP | CD4-positive, alpha-beta T cell differentiation involved in immune response | 18/2218 | 68/18723 | 7.29e-04 | 5.94e-03 | 18 |
| GO:0002287 | Oral cavity | EOLP | alpha-beta T cell activation involved in immune response | 18/2218 | 69/18723 | 8.79e-04 | 6.75e-03 | 18 |
| GO:0002293 | Oral cavity | EOLP | alpha-beta T cell differentiation involved in immune response | 18/2218 | 69/18723 | 8.79e-04 | 6.75e-03 | 18 |
| GO:0002292 | Oral cavity | EOLP | T cell differentiation involved in immune response | 19/2218 | 75/18723 | 9.43e-04 | 7.15e-03 | 19 |
| GO:00341211 | Oral cavity | EOLP | regulation of toll-like receptor signaling pathway | 19/2218 | 75/18723 | 9.43e-04 | 7.15e-03 | 19 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0465923 | Oral cavity | EOLP | Th17 cell differentiation | 41/1218 | 108/8465 | 9.84e-10 | 3.18e-08 | 1.87e-08 | 41 |
| hsa0465933 | Oral cavity | EOLP | Th17 cell differentiation | 41/1218 | 108/8465 | 9.84e-10 | 3.18e-08 | 1.87e-08 | 41 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| IRF4 | PLA | Colorectum | ADJ | SSR4,UBE2J1,ARSG, etc. | 2.04e-01 |  |
| IRF4 | pDC | Lung | ADJ | TCF4,SLC15A4,C12orf75, etc. | 7.37e-02 |  |
| IRF4 | BN | Lung | ADJ | TCF4,SLC15A4,C12orf75, etc. | 4.09e-02 | |
| IRF4 | MEN | Skin | ADJ | ROBO2,AC007319.1,INPP4B, etc. | 3.90e-01 |  |
| IRF4 | MEN | Skin | AK | ROBO2,AC007319.1,INPP4B, etc. | 3.78e-01 |  |
| IRF4 | MEN | Skin | cSCC | ROBO2,AC007319.1,INPP4B, etc. | 1.74e-01 |  |
| IRF4 | MEN | Skin | SCCIS | ROBO2,AC007319.1,INPP4B, etc. | 1.97e-01 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| IRF4 | insertion | Frame_Shift_Ins | novel | c.363_364insCCTCTGTCTAGAGCTGTCTCCCTTGCCC | p.Tyr122ProfsTer18 | p.Y122Pfs*18 | Q15306 | protein_coding | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| IRF4 | SNV | Missense_Mutation | rs751010198 | c.737C>T | p.Ala246Val | p.A246V | Q15306 | protein_coding | tolerated(0.09) | benign(0.062) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| IRF4 | SNV | Missense_Mutation | c.256N>A | p.Asp86Asn | p.D86N | Q15306 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| IRF4 | SNV | Missense_Mutation | c.967N>A | p.Gly323Arg | p.G323R | Q15306 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3693-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| IRF4 | SNV | Missense_Mutation | c.1304N>A | p.Ser435Asn | p.S435N | Q15306 | protein_coding | tolerated(0.57) | benign(0.001) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| IRF4 | SNV | Missense_Mutation | c.103G>A | p.Gly35Ser | p.G35S | Q15306 | protein_coding | deleterious(0.04) | benign(0.095) | TCGA-AA-3851-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| IRF4 | SNV | Missense_Mutation | novel | c.1004N>C | p.Tyr335Ser | p.Y335S | Q15306 | protein_coding | deleterious(0) | probably_damaging(0.944) | TCGA-AA-A01I-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| IRF4 | SNV | Missense_Mutation | rs143144957 | c.604G>A | p.Gly202Ser | p.G202S | Q15306 | protein_coding | tolerated(1) | benign(0) | TCGA-G4-6315-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | SD |
| IRF4 | insertion | Frame_Shift_Ins | novel | c.401_402insC | p.Lys134AsnfsTer78 | p.K134Nfs*78 | Q15306 | protein_coding | TCGA-AA-A01K-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folinic | CR | ||
| IRF4 | SNV | Missense_Mutation | rs781586995 | c.544N>A | p.Val182Ile | p.V182I | Q15306 | protein_coding | tolerated(0.36) | benign(0.018) | TCGA-A5-AB3J-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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