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Gene: BCDIN3D |
Gene summary for BCDIN3D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BCDIN3D | Gene ID | 144233 |
| Gene name | BCDIN3 domain containing RNA methyltransferase | |
| Gene Alias | BCDIN3D | |
| Cytomap | 12q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | Q7Z5W3 |
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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 |
| 144233 | BCDIN3D | HCC1_Meng | Human | Liver | HCC | 4.42e-37 | 8.97e-03 | 0.0246 |
| 144233 | BCDIN3D | HCC2_Meng | Human | Liver | HCC | 9.02e-05 | -6.95e-03 | 0.0107 |
| 144233 | BCDIN3D | HCC2 | Human | Liver | HCC | 2.30e-06 | 2.31e+00 | 0.5341 |
| 144233 | BCDIN3D | HCC5 | Human | Liver | HCC | 3.64e-04 | 5.62e-01 | 0.4932 |
| 144233 | BCDIN3D | S014 | Human | Liver | HCC | 3.73e-03 | 2.30e-01 | 0.2254 |
| 144233 | BCDIN3D | S016 | Human | Liver | HCC | 2.47e-03 | 2.34e-01 | 0.2243 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:0008033 | Liver | HCC | tRNA processing | 87/7958 | 127/18723 | 2.66e-09 | 7.23e-08 | 87 |
| GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
| GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| GO:0006400 | Liver | HCC | tRNA modification | 60/7958 | 90/18723 | 3.09e-06 | 4.09e-05 | 60 |
| GO:003105021 | Liver | HCC | dsRNA processing | 38/7958 | 54/18723 | 3.15e-05 | 3.21e-04 | 38 |
| GO:007091821 | Liver | HCC | production of small RNA involved in gene silencing by RNA | 38/7958 | 54/18723 | 3.15e-05 | 3.21e-04 | 38 |
| GO:001058611 | Liver | HCC | miRNA metabolic process | 22/7958 | 27/18723 | 3.97e-05 | 3.90e-04 | 22 |
| GO:0001510 | Liver | HCC | RNA methylation | 53/7958 | 83/18723 | 6.96e-05 | 6.29e-04 | 53 |
| GO:003519621 | Liver | HCC | production of miRNAs involved in gene silencing by miRNA | 36/7958 | 52/18723 | 8.79e-05 | 7.66e-04 | 36 |
| GO:00310541 | Liver | HCC | pre-miRNA processing | 13/7958 | 14/18723 | 1.25e-04 | 1.03e-03 | 13 |
| GO:0030488 | Liver | HCC | tRNA methylation | 29/7958 | 41/18723 | 2.38e-04 | 1.79e-03 | 29 |
| GO:006096621 | Liver | HCC | regulation of gene silencing by RNA | 35/7958 | 53/18723 | 4.59e-04 | 3.04e-03 | 35 |
| GO:006014721 | Liver | HCC | regulation of posttranscriptional gene silencing | 34/7958 | 52/18723 | 7.24e-04 | 4.42e-03 | 34 |
| GO:006096411 | Liver | HCC | regulation of gene silencing by miRNA | 31/7958 | 49/18723 | 2.70e-03 | 1.29e-02 | 31 |
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| 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 |
| BCDIN3D | SNV | Missense_Mutation | c.305N>C | p.Arg102Thr | p.R102T | Q7Z5W3 | protein_coding | tolerated(0.47) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| BCDIN3D | insertion | Frame_Shift_Ins | novel | c.200_201insACCATCTGTCTTAGGAATCTCTCTTGGAGAGGAGT | p.Ile68ProfsTer12 | p.I68Pfs*12 | Q7Z5W3 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| BCDIN3D | SNV | Missense_Mutation | novel | c.307N>C | p.Glu103Gln | p.E103Q | Q7Z5W3 | protein_coding | tolerated(0.06) | benign(0.116) | TCGA-ZJ-AB0I-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| BCDIN3D | SNV | Missense_Mutation | c.458N>G | p.Phe153Cys | p.F153C | Q7Z5W3 | protein_coding | deleterious(0.05) | possibly_damaging(0.635) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| BCDIN3D | SNV | Missense_Mutation | c.409N>G | p.Met137Val | p.M137V | Q7Z5W3 | protein_coding | tolerated(0.09) | benign(0.007) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
| BCDIN3D | SNV | Missense_Mutation | c.326N>A | p.Cys109Tyr | p.C109Y | Q7Z5W3 | protein_coding | deleterious(0.01) | benign(0.028) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BCDIN3D | SNV | Missense_Mutation | rs772541621 | c.358N>A | p.Glu120Lys | p.E120K | Q7Z5W3 | protein_coding | tolerated(0.52) | benign(0) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| BCDIN3D | insertion | Frame_Shift_Ins | novel | c.309_310insCC | p.Phe104ProfsTer9 | p.F104Pfs*9 | Q7Z5W3 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| BCDIN3D | SNV | Missense_Mutation | rs764721935 | c.463N>T | p.Arg155Cys | p.R155C | Q7Z5W3 | protein_coding | tolerated(0.2) | benign(0) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| BCDIN3D | SNV | Missense_Mutation | novel | c.419N>T | p.Arg140Met | p.R140M | Q7Z5W3 | protein_coding | tolerated(0.1) | benign(0.145) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | 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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