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Gene: DPF3 |
Gene summary for DPF3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DPF3 | Gene ID | 8110 |
| Gene name | double PHD fingers 3 | |
| Gene Alias | BAF45C | |
| Cytomap | 14q24.2 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q92784 |
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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 |
| 8110 | DPF3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.92e-24 | -6.98e-01 | 0.0155 |
| 8110 | DPF3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.19e-04 | -4.87e-01 | -0.1808 |
| 8110 | DPF3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.23e-05 | -4.97e-01 | -0.0811 |
| 8110 | DPF3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 8.51e-06 | -5.93e-01 | -0.1207 |
| 8110 | DPF3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.55e-04 | -3.44e-01 | -0.1464 |
| 8110 | DPF3 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.91e-09 | -3.87e-01 | -0.1001 |
| 8110 | DPF3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 7.71e-03 | -4.07e-01 | -0.0179 |
| 8110 | DPF3 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.27e-14 | -6.47e-01 | 0.096 |
| 8110 | DPF3 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.31e-07 | -5.93e-01 | 0.0338 |
| 8110 | DPF3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.97e-24 | -6.03e-01 | 0.0674 |
| 8110 | DPF3 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.63e-02 | -5.94e-01 | 0.0112 |
| 8110 | DPF3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.81e-26 | -6.51e-01 | 0.294 |
| 8110 | DPF3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 8.36e-09 | -6.73e-01 | 0.281 |
| 8110 | DPF3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.46e-41 | -7.73e-01 | 0.3859 |
| 8110 | DPF3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.42e-11 | -7.79e-01 | 0.2585 |
| 8110 | DPF3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.29e-40 | -7.81e-01 | 0.3005 |
| 8110 | DPF3 | F007 | Human | Colorectum | FAP | 3.15e-13 | -6.60e-01 | 0.1176 |
| 8110 | DPF3 | A002-C-010 | Human | Colorectum | FAP | 1.06e-26 | -6.52e-01 | 0.242 |
| 8110 | DPF3 | A001-C-207 | Human | Colorectum | FAP | 6.17e-15 | -6.17e-01 | 0.1278 |
| 8110 | DPF3 | A015-C-203 | Human | Colorectum | FAP | 1.39e-31 | -5.76e-01 | -0.1294 |
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| 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 |
| ∗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:0006325 | Colorectum | AD | chromatin organization | 119/3918 | 409/18723 | 4.85e-05 | 8.33e-04 | 119 |
| GO:00063251 | Colorectum | SER | chromatin organization | 89/2897 | 409/18723 | 4.15e-04 | 6.17e-03 | 89 |
| GO:00063252 | Colorectum | MSS | chromatin organization | 107/3467 | 409/18723 | 7.22e-05 | 1.21e-03 | 107 |
| GO:00063253 | Colorectum | FAP | chromatin organization | 84/2622 | 409/18723 | 1.62e-04 | 2.47e-03 | 84 |
| GO:00063254 | Colorectum | CRC | chromatin organization | 74/2078 | 409/18723 | 1.48e-05 | 4.61e-04 | 74 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04714 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
| hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
| hsa047141 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
| hsa052251 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
| hsa047142 | Colorectum | SER | Thermogenesis | 106/1580 | 232/8465 | 1.15e-21 | 6.34e-20 | 4.61e-20 | 106 |
| hsa047143 | Colorectum | SER | Thermogenesis | 106/1580 | 232/8465 | 1.15e-21 | 6.34e-20 | 4.61e-20 | 106 |
| hsa047144 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
| hsa052252 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
| hsa047145 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
| hsa052253 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
| hsa047148 | Colorectum | FAP | Thermogenesis | 70/1404 | 232/8465 | 1.38e-07 | 3.08e-06 | 1.87e-06 | 70 |
| hsa052254 | Colorectum | FAP | Hepatocellular carcinoma | 43/1404 | 168/8465 | 1.78e-03 | 8.99e-03 | 5.47e-03 | 43 |
| hsa047149 | Colorectum | FAP | Thermogenesis | 70/1404 | 232/8465 | 1.38e-07 | 3.08e-06 | 1.87e-06 | 70 |
| hsa052255 | Colorectum | FAP | Hepatocellular carcinoma | 43/1404 | 168/8465 | 1.78e-03 | 8.99e-03 | 5.47e-03 | 43 |
| hsa052256 | Colorectum | CRC | Hepatocellular carcinoma | 37/1091 | 168/8465 | 6.38e-04 | 5.89e-03 | 3.99e-03 | 37 |
| hsa052257 | Colorectum | CRC | Hepatocellular carcinoma | 37/1091 | 168/8465 | 6.38e-04 | 5.89e-03 | 3.99e-03 | 37 |
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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 |
| DPF3 | SNV | Missense_Mutation | rs369169805 | c.532N>T | p.Arg178Cys | p.R178C | protein_coding | tolerated(0.16) | probably_damaging(0.988) | TCGA-GI-A2C8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Adriamycin | SD | |
| DPF3 | insertion | Nonsense_Mutation | novel | c.863_864insCATAGATGTACACATACATGAATGAAGGGAGGGCAGCT | p.Gln288HisfsTer9 | p.Q288Hfs*9 | protein_coding | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| DPF3 | insertion | Nonsense_Mutation | novel | c.791_792insAGATACACTCAGAAGCATACCATTGTGACTACTTAAATG | p.Asn264delinsLysAspThrLeuArgSerIleProLeuTerLeuLeuLysCys | p.N264delinsKDTLRSIPL*LLKC | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||||
| DPF3 | SNV | Missense_Mutation | rs757444001 | c.1031G>A | p.Arg344His | p.R344H | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-C5-A8XI-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD | |
| DPF3 | SNV | Missense_Mutation | c.625N>A | p.Glu209Lys | p.E209K | protein_coding | tolerated(0.11) | benign(0.373) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | ||
| DPF3 | SNV | Missense_Mutation | rs372100997 | c.760G>A | p.Val254Ile | p.V254I | protein_coding | deleterious(0.05) | possibly_damaging(0.459) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| DPF3 | SNV | Missense_Mutation | c.1145N>A | p.Gly382Asp | p.G382D | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.996) | TCGA-AA-3655-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| DPF3 | SNV | Missense_Mutation | c.869N>A | p.Thr290Asn | p.T290N | protein_coding | tolerated(0.25) | benign(0.003) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | ||
| DPF3 | SNV | Missense_Mutation | c.642G>T | p.Glu214Asp | p.E214D | protein_coding | tolerated(0.31) | benign(0.006) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| DPF3 | SNV | Missense_Mutation | rs780037884 | c.1130N>T | p.Thr377Met | p.T377M | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.738) | TCGA-AG-A02G-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | PD |
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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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