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Gene: ILF3 |
Gene summary for ILF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ILF3 | Gene ID | 3609 |
| Gene name | interleukin enhancer binding factor 3 | |
| Gene Alias | CBTF | |
| Cytomap | 19p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | Q12906 |
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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 |
| 3609 | ILF3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.74e-02 | -1.97e-01 | 0.0155 |
| 3609 | ILF3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.61e-02 | 3.28e-02 | 0.0588 |
| 3609 | ILF3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.90e-13 | 5.94e-01 | 0.294 |
| 3609 | ILF3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 7.62e-03 | 4.21e-01 | 0.3859 |
| 3609 | ILF3 | A015-C-203 | Human | Colorectum | FAP | 1.82e-18 | 1.21e-01 | -0.1294 |
| 3609 | ILF3 | A002-C-201 | Human | Colorectum | FAP | 2.11e-03 | 1.03e-01 | 0.0324 |
| 3609 | ILF3 | A001-C-119 | Human | Colorectum | FAP | 9.24e-03 | 2.94e-01 | -0.1557 |
| 3609 | ILF3 | A001-C-108 | Human | Colorectum | FAP | 4.83e-12 | 2.91e-01 | -0.0272 |
| 3609 | ILF3 | A002-C-021 | Human | Colorectum | FAP | 1.86e-04 | 3.44e-01 | 0.1171 |
| 3609 | ILF3 | A002-C-205 | Human | Colorectum | FAP | 1.52e-11 | 2.50e-01 | -0.1236 |
| 3609 | ILF3 | A014-C-108 | Human | Colorectum | FAP | 5.89e-06 | 5.07e-01 | -0.124 |
| 3609 | ILF3 | A001-C-104 | Human | Colorectum | FAP | 3.90e-10 | 4.77e-01 | 0.0184 |
| 3609 | ILF3 | A015-C-006 | Human | Colorectum | FAP | 1.95e-13 | 4.93e-01 | -0.0994 |
| 3609 | ILF3 | A015-C-106 | Human | Colorectum | FAP | 6.29e-13 | 3.69e-01 | -0.0511 |
| 3609 | ILF3 | A002-C-114 | Human | Colorectum | FAP | 1.02e-10 | 2.74e-01 | -0.1561 |
| 3609 | ILF3 | A015-C-104 | Human | Colorectum | FAP | 3.95e-27 | 3.81e-01 | -0.1899 |
| 3609 | ILF3 | A015-C-202 | Human | Colorectum | FAP | 8.34e-05 | 3.80e-01 | -0.0849 |
| 3609 | ILF3 | A001-C-014 | Human | Colorectum | FAP | 3.71e-06 | 1.40e-02 | 0.0135 |
| 3609 | ILF3 | A002-C-016 | Human | Colorectum | FAP | 1.30e-08 | -1.67e-01 | 0.0521 |
| 3609 | ILF3 | A015-C-002 | Human | Colorectum | FAP | 2.57e-04 | 1.97e-01 | -0.0763 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:004506922 | Liver | HCC | regulation of viral genome replication | 59/7958 | 85/18723 | 4.66e-07 | 7.61e-06 | 59 |
| GO:00516071 | Liver | HCC | defense response to virus | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:01405461 | Liver | HCC | defense response to symbiont | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:004852511 | Liver | HCC | negative regulation of viral process | 59/7958 | 92/18723 | 2.28e-05 | 2.41e-04 | 59 |
| GO:003424921 | Liver | HCC | negative regulation of cellular amide metabolic process | 144/7958 | 273/18723 | 3.80e-04 | 2.61e-03 | 144 |
| GO:001714821 | Liver | HCC | negative regulation of translation | 129/7958 | 245/18723 | 8.14e-04 | 4.87e-03 | 129 |
| GO:00450711 | Liver | HCC | negative regulation of viral genome replication | 35/7958 | 56/18723 | 2.00e-03 | 1.01e-02 | 35 |
| GO:001603220 | Oral cavity | OSCC | viral process | 274/7305 | 415/18723 | 2.42e-29 | 1.70e-26 | 274 |
| GO:001905820 | Oral cavity | OSCC | viral life cycle | 208/7305 | 317/18723 | 4.59e-22 | 1.00e-19 | 208 |
| GO:000641720 | Oral cavity | OSCC | regulation of translation | 274/7305 | 468/18723 | 4.39e-18 | 4.63e-16 | 274 |
| GO:001907920 | Oral cavity | OSCC | viral genome replication | 95/7305 | 131/18723 | 6.35e-15 | 4.02e-13 | 95 |
| GO:000961515 | Oral cavity | OSCC | response to virus | 215/7305 | 367/18723 | 1.63e-14 | 9.41e-13 | 215 |
| GO:005079220 | Oral cavity | OSCC | regulation of viral process | 109/7305 | 164/18723 | 8.95e-13 | 4.10e-11 | 109 |
| GO:190390020 | Oral cavity | OSCC | regulation of viral life cycle | 97/7305 | 148/18723 | 5.34e-11 | 1.67e-09 | 97 |
| GO:00516074 | Oral cavity | OSCC | defense response to virus | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:01405464 | Oral cavity | OSCC | defense response to symbiont | 154/7305 | 265/18723 | 1.96e-10 | 5.63e-09 | 154 |
| GO:004506917 | Oral cavity | OSCC | regulation of viral genome replication | 62/7305 | 85/18723 | 2.14e-10 | 6.04e-09 | 62 |
| GO:00450717 | Oral cavity | OSCC | negative regulation of viral genome replication | 38/7305 | 56/18723 | 1.15e-05 | 1.18e-04 | 38 |
| GO:00485259 | Oral cavity | OSCC | negative regulation of viral process | 56/7305 | 92/18723 | 1.77e-05 | 1.72e-04 | 56 |
| GO:00342495 | Oral cavity | OSCC | negative regulation of cellular amide metabolic process | 130/7305 | 273/18723 | 2.20e-03 | 1.00e-02 | 130 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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 |
| ∗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. |
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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 |
| ILF3 | SNV | Missense_Mutation | c.188N>G | p.Asp63Gly | p.D63G | Q12906 | protein_coding | tolerated(0.08) | benign(0.114) | TCGA-A2-A259-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| ILF3 | SNV | Missense_Mutation | c.1164N>C | p.Lys388Asn | p.K388N | Q12906 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| ILF3 | SNV | Missense_Mutation | c.2638N>C | p.Ser880Pro | p.S880P | Q12906 | protein_coding | tolerated_low_confidence(0.26) | benign(0.192) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| ILF3 | SNV | Missense_Mutation | c.109N>G | p.His37Asp | p.H37D | Q12906 | protein_coding | tolerated(0.13) | probably_damaging(0.99) | TCGA-E2-A14Z-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | PD | |
| ILF3 | SNV | Missense_Mutation | c.2243N>G | p.Ser748Cys | p.S748C | Q12906 | protein_coding | deleterious(0.01) | possibly_damaging(0.634) | TCGA-EW-A1J6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD | |
| ILF3 | insertion | Frame_Shift_Ins | novel | c.2555_2556insGATGCCTTTGACAGTGATGAAAACGATTT | p.Lys853MetfsTer51 | p.K853Mfs*51 | Q12906 | protein_coding | TCGA-AN-A0FT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ILF3 | insertion | Frame_Shift_Ins | novel | c.713_714insCTCAACAAATTCGACCCCAAAAGAGGCTGAGACTGAGT | p.Arg239SerfsTer59 | p.R239Sfs*59 | Q12906 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ILF3 | SNV | Missense_Mutation | novel | c.1421N>T | p.Arg474Met | p.R474M | Q12906 | protein_coding | deleterious(0) | possibly_damaging(0.742) | TCGA-IR-A3LF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| ILF3 | SNV | Missense_Mutation | novel | c.634N>A | p.His212Asn | p.H212N | Q12906 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ILF3 | SNV | Missense_Mutation | c.1103N>T | p.Thr368Met | p.T368M | Q12906 | protein_coding | tolerated(0.11) | possibly_damaging(0.78) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| 3609 | ILF3 | KINASE, TRANSCRIPTION FACTOR | CSA | CYCLOSPORINE | 9843854 | |
| 3609 | ILF3 | KINASE, TRANSCRIPTION FACTOR | IL-2 | ALDESLEUKIN | 12504009 |
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