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Gene: WDR12 |
Gene summary for WDR12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | WDR12 | Gene ID | 55759 |
| Gene name | WD repeat domain 12 | |
| Gene Alias | YTM1 | |
| Cytomap | 2q33.2 | |
| Gene Type | protein-coding | GO ID | GO:0000460 | UniProtAcc | Q53T99 |
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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 |
| 55759 | WDR12 | LZE4T | Human | Esophagus | ESCC | 1.39e-03 | 1.06e-01 | 0.0811 |
| 55759 | WDR12 | LZE24T | Human | Esophagus | ESCC | 4.99e-11 | 2.04e-01 | 0.0596 |
| 55759 | WDR12 | LZE21T | Human | Esophagus | ESCC | 4.92e-02 | 1.70e-01 | 0.0655 |
| 55759 | WDR12 | LZE6T | Human | Esophagus | ESCC | 1.04e-03 | 6.54e-02 | 0.0845 |
| 55759 | WDR12 | P2T-E | Human | Esophagus | ESCC | 3.17e-16 | 2.41e-01 | 0.1177 |
| 55759 | WDR12 | P4T-E | Human | Esophagus | ESCC | 5.84e-23 | 6.79e-01 | 0.1323 |
| 55759 | WDR12 | P5T-E | Human | Esophagus | ESCC | 1.03e-21 | 4.99e-01 | 0.1327 |
| 55759 | WDR12 | P8T-E | Human | Esophagus | ESCC | 1.66e-14 | 8.55e-02 | 0.0889 |
| 55759 | WDR12 | P9T-E | Human | Esophagus | ESCC | 1.87e-12 | 2.67e-01 | 0.1131 |
| 55759 | WDR12 | P10T-E | Human | Esophagus | ESCC | 3.35e-28 | 3.98e-01 | 0.116 |
| 55759 | WDR12 | P11T-E | Human | Esophagus | ESCC | 5.14e-14 | 4.20e-01 | 0.1426 |
| 55759 | WDR12 | P12T-E | Human | Esophagus | ESCC | 3.09e-28 | 5.35e-01 | 0.1122 |
| 55759 | WDR12 | P15T-E | Human | Esophagus | ESCC | 1.86e-16 | 3.56e-01 | 0.1149 |
| 55759 | WDR12 | P16T-E | Human | Esophagus | ESCC | 2.13e-21 | 3.99e-01 | 0.1153 |
| 55759 | WDR12 | P17T-E | Human | Esophagus | ESCC | 2.82e-12 | 2.80e-01 | 0.1278 |
| 55759 | WDR12 | P19T-E | Human | Esophagus | ESCC | 5.24e-03 | 2.08e-01 | 0.1662 |
| 55759 | WDR12 | P20T-E | Human | Esophagus | ESCC | 4.02e-09 | 3.21e-01 | 0.1124 |
| 55759 | WDR12 | P21T-E | Human | Esophagus | ESCC | 1.36e-23 | 6.29e-01 | 0.1617 |
| 55759 | WDR12 | P22T-E | Human | Esophagus | ESCC | 1.81e-14 | 2.03e-01 | 0.1236 |
| 55759 | WDR12 | P23T-E | Human | Esophagus | ESCC | 1.00e-12 | 3.37e-01 | 0.108 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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: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:0042273111 | Esophagus | ESCC | ribosomal large subunit biogenesis | 65/8552 | 72/18723 | 1.53e-15 | 9.82e-14 | 65 |
| GO:000047016 | Esophagus | ESCC | maturation of LSU-rRNA | 27/8552 | 28/18723 | 9.94e-09 | 2.00e-07 | 27 |
| GO:00004603 | Esophagus | ESCC | maturation of 5.8S rRNA | 30/8552 | 35/18723 | 1.07e-06 | 1.34e-05 | 30 |
| GO:00004634 | Esophagus | ESCC | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 15/8552 | 15/18723 | 7.81e-06 | 7.69e-05 | 15 |
| GO:00072197 | Esophagus | ESCC | Notch signaling pathway | 106/8552 | 172/18723 | 1.74e-05 | 1.55e-04 | 106 |
| GO:00004663 | Esophagus | ESCC | maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 21/8552 | 24/18723 | 2.57e-05 | 2.17e-04 | 21 |
| 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 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:004227322 | Liver | HCC | ribosomal large subunit biogenesis | 64/7958 | 72/18723 | 2.31e-16 | 2.03e-14 | 64 |
| GO:000047011 | Liver | HCC | maturation of LSU-rRNA | 26/7958 | 28/18723 | 2.82e-08 | 6.43e-07 | 26 |
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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 |
| WDR12 | SNV | Missense_Mutation | c.154G>C | p.Glu52Gln | p.E52Q | Q9GZL7 | protein_coding | deleterious(0.03) | possibly_damaging(0.784) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| WDR12 | SNV | Missense_Mutation | novel | c.236A>G | p.Glu79Gly | p.E79G | Q9GZL7 | protein_coding | tolerated(0.12) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| WDR12 | SNV | Missense_Mutation | c.645C>G | p.Ile215Met | p.I215M | Q9GZL7 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| WDR12 | SNV | Missense_Mutation | rs145165057 | c.419N>T | p.Thr140Met | p.T140M | Q9GZL7 | protein_coding | deleterious(0.04) | benign(0.397) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| WDR12 | SNV | Missense_Mutation | novel | c.514N>C | p.Trp172Arg | p.W172R | Q9GZL7 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| WDR12 | SNV | Missense_Mutation | novel | c.1262T>C | p.Val421Ala | p.V421A | Q9GZL7 | protein_coding | tolerated_low_confidence(0.48) | benign(0) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| WDR12 | SNV | Missense_Mutation | novel | c.1118N>T | p.Arg373Ile | p.R373I | Q9GZL7 | protein_coding | deleterious(0) | possibly_damaging(0.871) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| WDR12 | SNV | Missense_Mutation | rs767414812 | c.895G>A | p.Val299Met | p.V299M | Q9GZL7 | protein_coding | deleterious(0.04) | possibly_damaging(0.9) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| WDR12 | SNV | Missense_Mutation | c.246N>C | p.Glu82Asp | p.E82D | Q9GZL7 | protein_coding | tolerated(0.29) | benign(0.012) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| WDR12 | SNV | Missense_Mutation | c.536N>G | p.Val179Gly | p.V179G | Q9GZL7 | protein_coding | deleterious(0) | benign(0.129) | TCGA-AP-A0LT-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 |
| Page: 1 |
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