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Gene: DDB1 |
Gene summary for DDB1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DDB1 | Gene ID | 1642 |
| Gene name | damage specific DNA binding protein 1 | |
| Gene Alias | DDBA | |
| Cytomap | 11q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | Q16531 |
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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 |
| 1642 | DDB1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.78e-02 | 4.48e-01 | -0.1808 |
| 1642 | DDB1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.49e-08 | 5.70e-01 | -0.0811 |
| 1642 | DDB1 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.34e-04 | 4.36e-01 | -0.1088 |
| 1642 | DDB1 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.67e-18 | 6.09e-01 | -0.1954 |
| 1642 | DDB1 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.13e-03 | 6.05e-01 | -0.2602 |
| 1642 | DDB1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.40e-06 | 4.81e-01 | -0.1526 |
| 1642 | DDB1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.19e-06 | 4.33e-01 | -0.1464 |
| 1642 | DDB1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.35e-11 | 6.83e-01 | -0.059 |
| 1642 | DDB1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.57e-03 | 5.97e-01 | -0.1706 |
| 1642 | DDB1 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.33e-11 | 5.97e-01 | 0.096 |
| 1642 | DDB1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 5.40e-04 | 5.94e-01 | 0.0446 |
| 1642 | DDB1 | HTA11_6801_2000001011 | Human | Colorectum | SER | 9.38e-03 | 6.64e-01 | 0.0171 |
| 1642 | DDB1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.60e-03 | 4.04e-01 | 0.0674 |
| 1642 | DDB1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 8.52e-03 | 3.84e-01 | 0.0588 |
| 1642 | DDB1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.67e-12 | 5.74e-01 | 0.294 |
| 1642 | DDB1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 7.65e-04 | 9.94e-01 | 0.3487 |
| 1642 | DDB1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.71e-07 | 5.88e-01 | 0.281 |
| 1642 | DDB1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 8.05e-11 | 8.30e-01 | 0.3859 |
| 1642 | DDB1 | A015-C-203 | Human | Colorectum | FAP | 2.68e-07 | -1.81e-01 | -0.1294 |
| 1642 | DDB1 | A001-C-108 | Human | Colorectum | FAP | 3.82e-05 | -1.41e-01 | -0.0272 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
| GO:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
| GO:0009896 | Colorectum | AD | positive regulation of catabolic process | 180/3918 | 492/18723 | 4.33e-16 | 1.94e-13 | 180 |
| GO:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
| GO:0019058 | Colorectum | AD | viral life cycle | 119/3918 | 317/18723 | 6.18e-12 | 8.23e-10 | 119 |
| GO:0045732 | Colorectum | AD | positive regulation of protein catabolic process | 92/3918 | 231/18723 | 3.85e-11 | 4.47e-09 | 92 |
| GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
| GO:0044403 | Colorectum | AD | biological process involved in symbiotic interaction | 99/3918 | 290/18723 | 1.02e-07 | 4.93e-06 | 99 |
| GO:0051701 | Colorectum | AD | biological process involved in interaction with host | 73/3918 | 203/18723 | 5.08e-07 | 1.88e-05 | 73 |
| GO:0048524 | Colorectum | AD | positive regulation of viral process | 31/3918 | 65/18723 | 1.33e-06 | 4.23e-05 | 31 |
| GO:0019079 | Colorectum | AD | viral genome replication | 51/3918 | 131/18723 | 1.83e-06 | 5.51e-05 | 51 |
| GO:0052126 | Colorectum | AD | movement in host environment | 63/3918 | 175/18723 | 2.85e-06 | 8.11e-05 | 63 |
| GO:0007623 | Colorectum | AD | circadian rhythm | 72/3918 | 210/18723 | 4.50e-06 | 1.21e-04 | 72 |
| GO:0050792 | Colorectum | AD | regulation of viral process | 59/3918 | 164/18723 | 5.95e-06 | 1.52e-04 | 59 |
| GO:0048511 | Colorectum | AD | rhythmic process | 94/3918 | 298/18723 | 1.00e-05 | 2.34e-04 | 94 |
| GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
| GO:0019318 | Colorectum | AD | hexose metabolic process | 77/3918 | 237/18723 | 1.96e-05 | 4.01e-04 | 77 |
| GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
| GO:0044262 | Colorectum | AD | cellular carbohydrate metabolic process | 87/3918 | 283/18723 | 6.00e-05 | 1.01e-03 | 87 |
| GO:0005996 | Colorectum | AD | monosaccharide metabolic process | 80/3918 | 257/18723 | 7.31e-05 | 1.17e-03 | 80 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04120 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa05170 | Colorectum | AD | Human immunodeficiency virus 1 infection | 72/2092 | 212/8465 | 1.40e-03 | 8.46e-03 | 5.39e-03 | 72 |
| hsa041201 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa051701 | Colorectum | AD | Human immunodeficiency virus 1 infection | 72/2092 | 212/8465 | 1.40e-03 | 8.46e-03 | 5.39e-03 | 72 |
| hsa051702 | Colorectum | SER | Human immunodeficiency virus 1 infection | 58/1580 | 212/8465 | 1.08e-03 | 8.56e-03 | 6.21e-03 | 58 |
| hsa041202 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa051703 | Colorectum | SER | Human immunodeficiency virus 1 infection | 58/1580 | 212/8465 | 1.08e-03 | 8.56e-03 | 6.21e-03 | 58 |
| hsa041203 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa041204 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa051704 | Colorectum | MSS | Human immunodeficiency virus 1 infection | 69/1875 | 212/8465 | 2.66e-04 | 1.98e-03 | 1.21e-03 | 69 |
| hsa05161 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
| hsa041205 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa051705 | Colorectum | MSS | Human immunodeficiency virus 1 infection | 69/1875 | 212/8465 | 2.66e-04 | 1.98e-03 | 1.21e-03 | 69 |
| hsa051611 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
| hsa041206 | Colorectum | FAP | Ubiquitin mediated proteolysis | 51/1404 | 142/8465 | 1.55e-08 | 5.84e-07 | 3.55e-07 | 51 |
| hsa051706 | Colorectum | FAP | Human immunodeficiency virus 1 infection | 51/1404 | 212/8465 | 2.98e-03 | 1.29e-02 | 7.87e-03 | 51 |
| hsa041207 | Colorectum | FAP | Ubiquitin mediated proteolysis | 51/1404 | 142/8465 | 1.55e-08 | 5.84e-07 | 3.55e-07 | 51 |
| hsa051707 | Colorectum | FAP | Human immunodeficiency virus 1 infection | 51/1404 | 212/8465 | 2.98e-03 | 1.29e-02 | 7.87e-03 | 51 |
| hsa034205 | Esophagus | HGIN | Nucleotide excision repair | 29/1383 | 63/8465 | 2.96e-08 | 5.36e-07 | 4.26e-07 | 29 |
| hsa0412026 | Esophagus | HGIN | Ubiquitin mediated proteolysis | 49/1383 | 142/8465 | 7.78e-08 | 1.33e-06 | 1.06e-06 | 49 |
| Page: 1 2 3 4 5 |
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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 |
| DDB1 | SNV | Missense_Mutation | c.2246C>T | p.Thr749Met | p.T749M | Q16531 | protein_coding | tolerated(0.22) | benign(0.003) | TCGA-HU-8604-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | doxifluridine | SD | |
| DDB1 | SNV | Missense_Mutation | c.185N>T | p.Ala62Val | p.A62V | Q16531 | protein_coding | deleterious(0.01) | benign(0.382) | TCGA-HU-A4GT-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | copolang | SD | |
| DDB1 | SNV | Missense_Mutation | novel | c.980N>A | p.Arg327His | p.R327H | Q16531 | protein_coding | tolerated(0.08) | probably_damaging(0.947) | TCGA-MX-A5UJ-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| DDB1 | SNV | Missense_Mutation | novel | c.545N>G | p.Tyr182Cys | p.Y182C | Q16531 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-VQ-A8E3-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| DDB1 | SNV | Missense_Mutation | novel | c.3194N>C | p.Val1065Ala | p.V1065A | Q16531 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-VQ-A8PP-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
| DDB1 | deletion | Frame_Shift_Del | novel | c.3069delN | p.Thr1024HisfsTer13 | p.T1024Hfs*13 | Q16531 | protein_coding | TCGA-BR-8372-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | etoposide | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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 |
| 1642 | DDB1 | DNA REPAIR | inhibitor | CHEMBL468 | THALIDOMIDE | |
| 1642 | DDB1 | DNA REPAIR | inhibitor | CHEMBL43452 | POMALIDOMIDE | |
| 1642 | DDB1 | DNA REPAIR | inhibitor | CHEMBL848 | LENALIDOMIDE |
| Page: 1 |
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