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Gene: WDR3 |
Gene summary for WDR3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | WDR3 | Gene ID | 10885 |
| Gene name | WD repeat domain 3 | |
| Gene Alias | DIP2 | |
| Cytomap | 1p12 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q5TDG3 |
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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 |
| 10885 | WDR3 | LZE4T | Human | Esophagus | ESCC | 3.47e-05 | 1.06e-01 | 0.0811 |
| 10885 | WDR3 | LZE7T | Human | Esophagus | ESCC | 1.63e-02 | 1.43e-01 | 0.0667 |
| 10885 | WDR3 | LZE24T | Human | Esophagus | ESCC | 7.35e-05 | 1.06e-01 | 0.0596 |
| 10885 | WDR3 | P1T-E | Human | Esophagus | ESCC | 4.02e-03 | 1.89e-01 | 0.0875 |
| 10885 | WDR3 | P2T-E | Human | Esophagus | ESCC | 7.46e-14 | 2.61e-01 | 0.1177 |
| 10885 | WDR3 | P4T-E | Human | Esophagus | ESCC | 9.87e-13 | 3.09e-01 | 0.1323 |
| 10885 | WDR3 | P5T-E | Human | Esophagus | ESCC | 4.66e-10 | 2.08e-01 | 0.1327 |
| 10885 | WDR3 | P8T-E | Human | Esophagus | ESCC | 5.09e-07 | 6.84e-02 | 0.0889 |
| 10885 | WDR3 | P9T-E | Human | Esophagus | ESCC | 4.46e-09 | 2.02e-01 | 0.1131 |
| 10885 | WDR3 | P10T-E | Human | Esophagus | ESCC | 2.54e-19 | 2.02e-01 | 0.116 |
| 10885 | WDR3 | P11T-E | Human | Esophagus | ESCC | 9.88e-03 | 1.16e-01 | 0.1426 |
| 10885 | WDR3 | P12T-E | Human | Esophagus | ESCC | 3.44e-13 | 2.48e-01 | 0.1122 |
| 10885 | WDR3 | P15T-E | Human | Esophagus | ESCC | 1.42e-05 | 6.85e-02 | 0.1149 |
| 10885 | WDR3 | P16T-E | Human | Esophagus | ESCC | 4.36e-20 | 1.78e-01 | 0.1153 |
| 10885 | WDR3 | P19T-E | Human | Esophagus | ESCC | 2.57e-04 | 3.85e-01 | 0.1662 |
| 10885 | WDR3 | P20T-E | Human | Esophagus | ESCC | 1.16e-09 | 9.58e-02 | 0.1124 |
| 10885 | WDR3 | P21T-E | Human | Esophagus | ESCC | 3.64e-11 | 3.17e-01 | 0.1617 |
| 10885 | WDR3 | P22T-E | Human | Esophagus | ESCC | 2.81e-06 | 4.24e-02 | 0.1236 |
| 10885 | WDR3 | P23T-E | Human | Esophagus | ESCC | 4.61e-18 | 5.40e-01 | 0.108 |
| 10885 | WDR3 | P24T-E | Human | Esophagus | ESCC | 4.47e-10 | 1.11e-01 | 0.1287 |
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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 | ||
| 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:00311243 | Esophagus | HGIN | mRNA 3'-end processing | 18/2587 | 62/18723 | 1.37e-03 | 1.61e-02 | 18 |
| GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
| GO:00304904 | Esophagus | ESCC | maturation of SSU-rRNA | 45/8552 | 50/18723 | 5.07e-11 | 1.63e-09 | 45 |
| GO:003112412 | Esophagus | ESCC | mRNA 3'-end processing | 47/8552 | 62/18723 | 1.29e-06 | 1.58e-05 | 47 |
| GO:00311233 | Esophagus | ESCC | RNA 3'-end processing | 76/8552 | 116/18723 | 1.25e-05 | 1.15e-04 | 76 |
| GO:00063012 | Esophagus | ESCC | postreplication repair | 26/8552 | 31/18723 | 1.32e-05 | 1.21e-04 | 26 |
| GO:00063783 | Esophagus | ESCC | mRNA polyadenylation | 33/8552 | 44/18723 | 7.30e-05 | 5.49e-04 | 33 |
| GO:00436313 | Esophagus | ESCC | RNA polyadenylation | 33/8552 | 45/18723 | 1.54e-04 | 1.02e-03 | 33 |
| GO:0006301 | Liver | Cirrhotic | postreplication repair | 15/4634 | 31/18723 | 3.68e-03 | 2.02e-02 | 15 |
| GO:0031123 | Liver | Cirrhotic | RNA 3'-end processing | 42/4634 | 116/18723 | 3.85e-03 | 2.10e-02 | 42 |
| GO:0031124 | Liver | Cirrhotic | mRNA 3'-end processing | 25/4634 | 62/18723 | 4.90e-03 | 2.56e-02 | 25 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| WDR3 | SNV | Missense_Mutation | c.2075C>T | p.Ser692Leu | p.S692L | Q9UNX4 | protein_coding | deleterious(0) | benign(0.434) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| WDR3 | SNV | Missense_Mutation | c.1045N>G | p.Leu349Val | p.L349V | Q9UNX4 | protein_coding | deleterious(0.04) | possibly_damaging(0.556) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| WDR3 | SNV | Missense_Mutation | c.1462N>A | p.Leu488Met | p.L488M | Q9UNX4 | protein_coding | tolerated(0.07) | probably_damaging(0.952) | TCGA-B6-A0X4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| WDR3 | SNV | Missense_Mutation | novel | c.1681N>G | p.Gln561Glu | p.Q561E | Q9UNX4 | protein_coding | tolerated(0.31) | benign(0.179) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| WDR3 | SNV | Missense_Mutation | rs367631829 | c.2719N>G | p.Arg907Gly | p.R907G | Q9UNX4 | protein_coding | deleterious(0.03) | probably_damaging(0.986) | TCGA-S3-AA17-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD |
| WDR3 | SNV | Missense_Mutation | novel | c.1012N>C | p.Glu338Gln | p.E338Q | Q9UNX4 | protein_coding | tolerated(0.09) | benign(0.001) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| WDR3 | SNV | Missense_Mutation | novel | c.1502C>T | p.Ser501Phe | p.S501F | Q9UNX4 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| WDR3 | SNV | Missense_Mutation | c.842N>C | p.Arg281Thr | p.R281T | Q9UNX4 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| WDR3 | SNV | Missense_Mutation | novel | c.88N>G | p.Thr30Ala | p.T30A | Q9UNX4 | protein_coding | tolerated(0.23) | benign(0.003) | TCGA-AA-3520-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| WDR3 | SNV | Missense_Mutation | rs773144364 | c.19N>C | p.Tyr7His | p.Y7H | Q9UNX4 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | 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 |
| Page: 1 |
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