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Gene: WDR4 |
Gene summary for WDR4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | WDR4 | Gene ID | 10785 |
| Gene name | WD repeat domain 4 | |
| Gene Alias | GAMOS6 | |
| Cytomap | 21q22.3 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | P57081 |
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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 |
| 10785 | WDR4 | LZE8T | Human | Esophagus | ESCC | 1.10e-02 | 1.68e-01 | 0.067 |
| 10785 | WDR4 | LZE24T | Human | Esophagus | ESCC | 2.32e-20 | 4.57e-01 | 0.0596 |
| 10785 | WDR4 | P2T-E | Human | Esophagus | ESCC | 6.47e-06 | 9.31e-02 | 0.1177 |
| 10785 | WDR4 | P4T-E | Human | Esophagus | ESCC | 1.06e-14 | 3.06e-01 | 0.1323 |
| 10785 | WDR4 | P5T-E | Human | Esophagus | ESCC | 1.01e-13 | 2.66e-01 | 0.1327 |
| 10785 | WDR4 | P9T-E | Human | Esophagus | ESCC | 3.05e-07 | 1.61e-01 | 0.1131 |
| 10785 | WDR4 | P10T-E | Human | Esophagus | ESCC | 5.46e-16 | 3.29e-01 | 0.116 |
| 10785 | WDR4 | P11T-E | Human | Esophagus | ESCC | 3.25e-05 | 2.30e-01 | 0.1426 |
| 10785 | WDR4 | P12T-E | Human | Esophagus | ESCC | 2.29e-10 | 2.69e-01 | 0.1122 |
| 10785 | WDR4 | P15T-E | Human | Esophagus | ESCC | 4.01e-11 | 2.52e-01 | 0.1149 |
| 10785 | WDR4 | P16T-E | Human | Esophagus | ESCC | 5.03e-05 | 1.15e-01 | 0.1153 |
| 10785 | WDR4 | P17T-E | Human | Esophagus | ESCC | 2.60e-06 | 2.63e-01 | 0.1278 |
| 10785 | WDR4 | P19T-E | Human | Esophagus | ESCC | 3.75e-07 | 4.41e-01 | 0.1662 |
| 10785 | WDR4 | P20T-E | Human | Esophagus | ESCC | 2.32e-06 | 1.56e-01 | 0.1124 |
| 10785 | WDR4 | P21T-E | Human | Esophagus | ESCC | 5.65e-31 | 6.67e-01 | 0.1617 |
| 10785 | WDR4 | P22T-E | Human | Esophagus | ESCC | 1.78e-09 | 1.84e-01 | 0.1236 |
| 10785 | WDR4 | P23T-E | Human | Esophagus | ESCC | 7.44e-14 | 2.75e-01 | 0.108 |
| 10785 | WDR4 | P24T-E | Human | Esophagus | ESCC | 4.27e-08 | 2.39e-01 | 0.1287 |
| 10785 | WDR4 | P26T-E | Human | Esophagus | ESCC | 1.08e-09 | 2.43e-01 | 0.1276 |
| 10785 | WDR4 | P27T-E | Human | Esophagus | ESCC | 1.77e-05 | 1.94e-01 | 0.1055 |
| Page: 1 2 3 4 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00706465 | Thyroid | PTC | protein modification by small protein removal | 71/5968 | 157/18723 | 3.03e-04 | 2.12e-03 | 71 |
| GO:20007794 | Thyroid | PTC | regulation of double-strand break repair | 42/5968 | 85/18723 | 5.59e-04 | 3.56e-03 | 42 |
| GO:00065138 | Thyroid | PTC | protein monoubiquitination | 34/5968 | 67/18723 | 1.00e-03 | 5.98e-03 | 34 |
| GO:00063566 | Thyroid | PTC | regulation of transcription by RNA polymerase I | 20/5968 | 34/18723 | 1.07e-03 | 6.32e-03 | 20 |
| GO:00063026 | Thyroid | PTC | double-strand break repair | 103/5968 | 251/18723 | 1.30e-03 | 7.40e-03 | 103 |
| GO:20002342 | Thyroid | PTC | positive regulation of rRNA processing | 8/5968 | 10/18723 | 2.46e-03 | 1.27e-02 | 8 |
| GO:00063604 | Thyroid | PTC | transcription by RNA polymerase I | 28/5968 | 55/18723 | 2.55e-03 | 1.31e-02 | 28 |
| GO:20002322 | Thyroid | PTC | regulation of rRNA processing | 11/5968 | 16/18723 | 2.70e-03 | 1.36e-02 | 11 |
| GO:009008510 | Thyroid | PTC | regulation of protein deubiquitination | 9/5968 | 12/18723 | 2.72e-03 | 1.36e-02 | 9 |
| GO:00457396 | Thyroid | PTC | positive regulation of DNA repair | 35/5968 | 73/18723 | 2.98e-03 | 1.47e-02 | 35 |
| GO:00165794 | Thyroid | PTC | protein deubiquitination | 59/5968 | 139/18723 | 5.50e-03 | 2.50e-02 | 59 |
| GO:004654612 | Thyroid | PTC | development of primary male sexual characteristics | 60/5968 | 142/18723 | 5.79e-03 | 2.61e-02 | 60 |
| GO:00352648 | Thyroid | PTC | multicellular organism growth | 56/5968 | 132/18723 | 6.79e-03 | 2.92e-02 | 56 |
| GO:000858412 | Thyroid | PTC | male gonad development | 59/5968 | 141/18723 | 7.88e-03 | 3.33e-02 | 59 |
| GO:00448043 | Thyroid | PTC | autophagy of nucleus | 10/5968 | 16/18723 | 1.13e-02 | 4.49e-02 | 10 |
| GO:00459434 | Thyroid | PTC | positive regulation of transcription by RNA polymerase I | 13/5968 | 23/18723 | 1.25e-02 | 4.88e-02 | 13 |
| GO:002261334 | Thyroid | ATC | ribonucleoprotein complex biogenesis | 292/6293 | 463/18723 | 3.05e-39 | 9.63e-36 | 292 |
| GO:004225434 | Thyroid | ATC | ribosome biogenesis | 203/6293 | 299/18723 | 3.63e-34 | 4.59e-31 | 203 |
| GO:000636432 | Thyroid | ATC | rRNA processing | 157/6293 | 225/18723 | 9.02e-29 | 5.70e-26 | 157 |
| GO:001607232 | Thyroid | ATC | rRNA metabolic process | 161/6293 | 236/18723 | 1.02e-27 | 5.89e-25 | 161 |
| 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 |
| 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 |
| WDR4 | SNV | Missense_Mutation | c.504N>T | p.Lys168Asn | p.K168N | P57081 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A25C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| WDR4 | insertion | Frame_Shift_Ins | novel | c.197_198insCTCCCAAACT | p.Thr68GlnfsTer17 | p.T68Qfs*17 | P57081 | protein_coding | TCGA-AN-A0FF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| WDR4 | insertion | In_Frame_Ins | novel | c.195_196insACCTCAGGTGATCCGCTGGCCTCG | p.Leu65_Ala66insThrSerGlyAspProLeuAlaSer | p.L65_A66insTSGDPLAS | P57081 | protein_coding | TCGA-AN-A0FF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| WDR4 | insertion | In_Frame_Ins | novel | c.306_307insCCACCTTCCTCTTCGCTGTCCTTCCCTGTG | p.Ala102_Arg103insProProSerSerSerLeuSerPheProVal | p.A102_R103insPPSSSLSFPV | P57081 | protein_coding | TCGA-BH-A0HU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| WDR4 | deletion | Frame_Shift_Del | novel | c.735delN | p.Ala246ArgfsTer88 | p.A246Rfs*88 | P57081 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| WDR4 | SNV | Missense_Mutation | rs144346351 | c.238G>A | p.Asp80Asn | p.D80N | P57081 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD |
| WDR4 | SNV | Missense_Mutation | rs543569485 | c.604N>A | p.Gly202Arg | p.G202R | P57081 | protein_coding | tolerated(0.16) | benign(0.021) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| WDR4 | SNV | Missense_Mutation | novel | c.1096G>A | p.Asp366Asn | p.D366N | P57081 | protein_coding | deleterious(0.01) | probably_damaging(0.924) | TCGA-AA-A02Y-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| WDR4 | SNV | Missense_Mutation | c.14T>C | p.Val5Ala | p.V5A | P57081 | protein_coding | tolerated_low_confidence(1) | benign(0) | TCGA-D5-5539-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fu | PD | |
| WDR4 | deletion | Frame_Shift_Del | c.724delN | p.Gln242ArgfsTer92 | p.Q242Rfs*92 | P57081 | protein_coding | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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