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Gene: NIF3L1 |
Gene summary for NIF3L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NIF3L1 | Gene ID | 60491 |
| Gene name | NGG1 interacting factor 3 like 1 | |
| Gene Alias | ALS2CR1 | |
| Cytomap | 2q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | A0A024R3V7 |
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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 |
| 60491 | NIF3L1 | LZE4T | Human | Esophagus | ESCC | 9.05e-09 | 2.27e-01 | 0.0811 |
| 60491 | NIF3L1 | LZE7T | Human | Esophagus | ESCC | 5.96e-05 | 1.89e-01 | 0.0667 |
| 60491 | NIF3L1 | LZE8T | Human | Esophagus | ESCC | 4.54e-05 | 1.65e-01 | 0.067 |
| 60491 | NIF3L1 | LZE20T | Human | Esophagus | ESCC | 1.19e-08 | 2.37e-01 | 0.0662 |
| 60491 | NIF3L1 | LZE24T | Human | Esophagus | ESCC | 2.25e-12 | 3.18e-01 | 0.0596 |
| 60491 | NIF3L1 | LZE21T | Human | Esophagus | ESCC | 3.65e-03 | 1.82e-01 | 0.0655 |
| 60491 | NIF3L1 | P1T-E | Human | Esophagus | ESCC | 3.01e-05 | 3.24e-01 | 0.0875 |
| 60491 | NIF3L1 | P2T-E | Human | Esophagus | ESCC | 2.80e-28 | 4.74e-01 | 0.1177 |
| 60491 | NIF3L1 | P4T-E | Human | Esophagus | ESCC | 7.44e-32 | 7.22e-01 | 0.1323 |
| 60491 | NIF3L1 | P5T-E | Human | Esophagus | ESCC | 7.55e-19 | 4.30e-01 | 0.1327 |
| 60491 | NIF3L1 | P8T-E | Human | Esophagus | ESCC | 1.72e-18 | 3.64e-01 | 0.0889 |
| 60491 | NIF3L1 | P9T-E | Human | Esophagus | ESCC | 2.64e-09 | 1.97e-01 | 0.1131 |
| 60491 | NIF3L1 | P10T-E | Human | Esophagus | ESCC | 4.96e-18 | 3.57e-01 | 0.116 |
| 60491 | NIF3L1 | P11T-E | Human | Esophagus | ESCC | 2.32e-16 | 5.02e-01 | 0.1426 |
| 60491 | NIF3L1 | P12T-E | Human | Esophagus | ESCC | 1.09e-27 | 5.35e-01 | 0.1122 |
| 60491 | NIF3L1 | P15T-E | Human | Esophagus | ESCC | 1.83e-25 | 4.88e-01 | 0.1149 |
| 60491 | NIF3L1 | P16T-E | Human | Esophagus | ESCC | 6.53e-27 | 4.30e-01 | 0.1153 |
| 60491 | NIF3L1 | P17T-E | Human | Esophagus | ESCC | 5.11e-06 | 2.45e-01 | 0.1278 |
| 60491 | NIF3L1 | P20T-E | Human | Esophagus | ESCC | 1.39e-25 | 4.89e-01 | 0.1124 |
| 60491 | NIF3L1 | P21T-E | Human | Esophagus | ESCC | 1.53e-38 | 6.12e-01 | 0.1617 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ∗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 |
| NIF3L1 | SNV | Missense_Mutation | c.115N>A | p.Asp39Asn | p.D39N | Q9GZT8 | protein_coding | tolerated(0.25) | benign(0.033) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NIF3L1 | SNV | Missense_Mutation | novel | c.356N>T | p.Asn119Ile | p.N119I | Q9GZT8 | protein_coding | deleterious(0.01) | probably_damaging(0.954) | TCGA-AN-A0FJ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NIF3L1 | SNV | Missense_Mutation | c.46N>A | p.Val16Ile | p.V16I | Q9GZT8 | protein_coding | tolerated_low_confidence(0.43) | benign(0) | TCGA-EK-A2RO-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| NIF3L1 | SNV | Missense_Mutation | c.829C>T | p.His277Tyr | p.H277Y | Q9GZT8 | protein_coding | tolerated(0.12) | benign(0.019) | TCGA-FU-A3HY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NIF3L1 | SNV | Missense_Mutation | rs770827322 | c.803G>A | p.Arg268Gln | p.R268Q | Q9GZT8 | protein_coding | tolerated(0.07) | possibly_damaging(0.657) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| NIF3L1 | SNV | Missense_Mutation | rs748912388 | c.65A>G | p.Asn22Ser | p.N22S | Q9GZT8 | protein_coding | tolerated_low_confidence(1) | benign(0) | TCGA-EI-6883-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5fluorouracil+leucovorin | SD |
| NIF3L1 | SNV | Missense_Mutation | novel | c.532G>T | p.Asp178Tyr | p.D178Y | Q9GZT8 | protein_coding | deleterious(0.01) | benign(0.423) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| NIF3L1 | SNV | Missense_Mutation | novel | c.352N>A | p.Glu118Lys | p.E118K | Q9GZT8 | protein_coding | deleterious(0) | probably_damaging(0.927) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NIF3L1 | SNV | Missense_Mutation | novel | c.823N>A | p.Leu275Ile | p.L275I | Q9GZT8 | protein_coding | deleterious(0.04) | possibly_damaging(0.817) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NIF3L1 | SNV | Missense_Mutation | rs201241357 | c.344N>A | p.Arg115Gln | p.R115Q | Q9GZT8 | protein_coding | tolerated(0.24) | benign(0.035) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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