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Gene: DEPDC1B |
Gene summary for DEPDC1B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DEPDC1B | Gene ID | 55789 |
| Gene name | DEP domain containing 1B | |
| Gene Alias | BRCC3 | |
| Cytomap | 5q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0006928 | UniProtAcc | Q8WUY9 |
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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 |
| 55789 | DEPDC1B | HCC1_Meng | Human | Liver | HCC | 7.43e-33 | 5.55e-02 | 0.0246 |
| 55789 | DEPDC1B | S027 | Human | Liver | HCC | 3.57e-02 | 4.50e-01 | 0.2446 |
| 55789 | DEPDC1B | S028 | Human | Liver | HCC | 6.02e-11 | 5.42e-01 | 0.2503 |
| 55789 | DEPDC1B | S029 | Human | Liver | HCC | 3.50e-13 | 9.89e-01 | 0.2581 |
| 55789 | DEPDC1B | P5_S10_cSCC | Human | Skin | cSCC | 1.79e-02 | 7.20e-02 | -0.299 |
| 55789 | DEPDC1B | P4_cSCC | Human | Skin | cSCC | 3.67e-13 | 2.89e-01 | -0.00290000000000005 |
| 55789 | DEPDC1B | P10_cSCC | Human | Skin | cSCC | 5.14e-10 | 5.04e-01 | 0.1017 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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). |
| 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:019873821 | Liver | HCC | cell-cell signaling by wnt | 247/7958 | 446/18723 | 2.11e-08 | 4.96e-07 | 247 |
| GO:001605521 | Liver | HCC | Wnt signaling pathway | 245/7958 | 444/18723 | 3.68e-08 | 8.09e-07 | 245 |
| GO:003011121 | Liver | HCC | regulation of Wnt signaling pathway | 180/7958 | 328/18723 | 3.62e-06 | 4.72e-05 | 180 |
| GO:003017721 | Liver | HCC | positive regulation of Wnt signaling pathway | 81/7958 | 140/18723 | 1.73e-04 | 1.36e-03 | 81 |
| GO:001605524 | Skin | cSCC | Wnt signaling pathway | 158/4864 | 444/18723 | 3.80e-06 | 5.70e-05 | 158 |
| GO:019873824 | Skin | cSCC | cell-cell signaling by wnt | 158/4864 | 446/18723 | 5.08e-06 | 7.38e-05 | 158 |
| GO:003011124 | Skin | cSCC | regulation of Wnt signaling pathway | 117/4864 | 328/18723 | 5.80e-05 | 5.75e-04 | 117 |
| GO:003017724 | Skin | cSCC | positive regulation of Wnt signaling pathway | 55/4864 | 140/18723 | 3.72e-04 | 2.92e-03 | 55 |
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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 |
| DEPDC1B | SNV | Missense_Mutation | novel | c.175N>G | p.Cys59Gly | p.C59G | Q8WUY9 | protein_coding | tolerated(0.21) | benign(0) | TCGA-B6-A1KC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| DEPDC1B | SNV | Missense_Mutation | c.563N>T | p.Ser188Phe | p.S188F | Q8WUY9 | protein_coding | deleterious(0.02) | possibly_damaging(0.746) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| DEPDC1B | SNV | Missense_Mutation | c.592N>T | p.Leu198Phe | p.L198F | Q8WUY9 | protein_coding | deleterious(0) | benign(0.221) | TCGA-EA-A43B-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| DEPDC1B | insertion | Frame_Shift_Ins | novel | c.437_438insATCTCCCACCAGGCACTTCACAAGAGAACATCCCAGTGAG | p.Pro147SerfsTer20 | p.P147Sfs*20 | Q8WUY9 | protein_coding | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| DEPDC1B | SNV | Missense_Mutation | c.351G>T | p.Lys117Asn | p.K117N | Q8WUY9 | protein_coding | tolerated(0.22) | benign(0.029) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD | |
| DEPDC1B | SNV | Missense_Mutation | novel | c.1510N>G | p.Lys504Glu | p.K504E | Q8WUY9 | protein_coding | deleterious(0.02) | benign(0.066) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| DEPDC1B | SNV | Missense_Mutation | c.221A>C | p.Gln74Pro | p.Q74P | Q8WUY9 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| DEPDC1B | SNV | Missense_Mutation | c.1297C>A | p.Arg433Ser | p.R433S | Q8WUY9 | protein_coding | tolerated(0.11) | benign(0.018) | TCGA-CK-6747-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| DEPDC1B | SNV | Missense_Mutation | c.351N>T | p.Lys117Asn | p.K117N | Q8WUY9 | protein_coding | tolerated(0.22) | benign(0.029) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| DEPDC1B | SNV | Missense_Mutation | novel | c.796N>A | p.Gly266Arg | p.G266R | Q8WUY9 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A0G1-01 | 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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