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Gene: BNIP1 |
Gene summary for BNIP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BNIP1 | Gene ID | 662 |
| Gene name | BCL2 interacting protein 1 | |
| Gene Alias | NIP1 | |
| Cytomap | 5q35.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q12981 |
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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 |
| 662 | BNIP1 | SYSMH2 | Human | Oral cavity | OSCC | 9.71e-04 | 1.73e-01 | 0.2326 |
| 662 | BNIP1 | SYSMH3 | Human | Oral cavity | OSCC | 2.59e-07 | 2.27e-01 | 0.2442 |
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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 | ||
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:0031667111 | Esophagus | ESCC | response to nutrient levels | 289/8552 | 474/18723 | 9.25e-12 | 3.47e-10 | 289 |
| GO:0070482111 | Esophagus | ESCC | response to oxygen levels | 218/8552 | 347/18723 | 6.91e-11 | 2.17e-09 | 218 |
| GO:000689017 | Esophagus | ESCC | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 46/8552 | 52/18723 | 1.23e-10 | 3.66e-09 | 46 |
| GO:004259419 | Esophagus | ESCC | response to starvation | 133/8552 | 197/18723 | 4.31e-10 | 1.14e-08 | 133 |
| GO:0036293111 | Esophagus | ESCC | response to decreased oxygen levels | 201/8552 | 322/18723 | 8.37e-10 | 2.04e-08 | 201 |
| GO:000702914 | Esophagus | ESCC | endoplasmic reticulum organization | 65/8552 | 87/18723 | 3.28e-08 | 6.08e-07 | 65 |
| GO:00482844 | Esophagus | ESCC | organelle fusion | 94/8552 | 141/18723 | 3.72e-07 | 5.16e-06 | 94 |
| GO:00901743 | Esophagus | ESCC | organelle membrane fusion | 73/8552 | 110/18723 | 9.29e-06 | 8.88e-05 | 73 |
| GO:00610254 | Esophagus | ESCC | membrane fusion | 98/8552 | 163/18723 | 1.39e-04 | 9.41e-04 | 98 |
| GO:0090649 | Esophagus | ESCC | response to oxygen-glucose deprivation | 10/8552 | 11/18723 | 2.54e-03 | 1.08e-02 | 10 |
| GO:004819315 | Oral cavity | OSCC | Golgi vesicle transport | 209/7305 | 296/18723 | 1.39e-28 | 6.30e-26 | 209 |
| GO:007048219 | Oral cavity | OSCC | response to oxygen levels | 200/7305 | 347/18723 | 1.17e-12 | 5.13e-11 | 200 |
| GO:003629319 | Oral cavity | OSCC | response to decreased oxygen levels | 182/7305 | 322/18723 | 1.14e-10 | 3.41e-09 | 182 |
| GO:003166720 | Oral cavity | OSCC | response to nutrient levels | 245/7305 | 474/18723 | 1.02e-08 | 2.10e-07 | 245 |
| GO:000689010 | Oral cavity | OSCC | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 40/7305 | 52/18723 | 2.86e-08 | 5.50e-07 | 40 |
| GO:00070294 | Oral cavity | OSCC | endoplasmic reticulum organization | 58/7305 | 87/18723 | 1.59e-07 | 2.61e-06 | 58 |
| GO:004259416 | Oral cavity | OSCC | response to starvation | 111/7305 | 197/18723 | 5.68e-07 | 8.19e-06 | 111 |
| GO:00482843 | Oral cavity | OSCC | organelle fusion | 82/7305 | 141/18723 | 3.08e-06 | 3.72e-05 | 82 |
| GO:00901742 | Oral cavity | OSCC | organelle membrane fusion | 63/7305 | 110/18723 | 7.75e-05 | 6.01e-04 | 63 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041305 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
| hsa0413012 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
| hsa041304 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
| hsa0413011 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
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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 |
| BNIP1 | SNV | Missense_Mutation | novel | c.358N>G | p.Leu120Val | p.L120V | Q12981 | protein_coding | tolerated(0.09) | benign(0.138) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| BNIP1 | insertion | Frame_Shift_Ins | novel | c.130_131insCTTGGGTCCTGCCGCTGCCCGTAGCCGGCGTCCCC | p.Asn44ThrfsTer16 | p.N44Tfs*16 | Q12981 | protein_coding | TCGA-A8-A08J-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| BNIP1 | SNV | Missense_Mutation | c.539N>G | p.Thr180Ser | p.T180S | Q12981 | protein_coding | tolerated(0.61) | benign(0.003) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| BNIP1 | SNV | Missense_Mutation | c.752N>T | p.Ala251Val | p.A251V | Q12981 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| BNIP1 | SNV | Missense_Mutation | rs372735517 | c.691N>T | p.Arg231Trp | p.R231W | Q12981 | protein_coding | deleterious(0.01) | probably_damaging(0.993) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD |
| BNIP1 | SNV | Missense_Mutation | rs370583969 | c.448N>A | p.Asp150Asn | p.D150N | Q12981 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| BNIP1 | SNV | Missense_Mutation | novel | c.770N>A | p.Ala257Asp | p.A257D | Q12981 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| BNIP1 | SNV | Missense_Mutation | c.328G>A | p.Glu110Lys | p.E110K | Q12981 | protein_coding | deleterious(0.05) | probably_damaging(0.995) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| BNIP1 | SNV | Missense_Mutation | c.170N>T | p.Arg57Ile | p.R57I | Q12981 | protein_coding | deleterious(0) | possibly_damaging(0.898) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| BNIP1 | SNV | Missense_Mutation | rs777949267 | c.500N>T | p.Arg167Met | p.R167M | Q12981 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AX-A0J1-01 | 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 |
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