|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: ZC3H13 |
Gene summary for ZC3H13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ZC3H13 | Gene ID | 23091 |
| Gene name | zinc finger CCCH-type containing 13 | |
| Gene Alias | KIAA0853 | |
| Cytomap | 13q14.13 | |
| Gene Type | protein-coding | GO ID | GO:0001510 | UniProtAcc | A0PJJ2 |
Top |
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 |
| 23091 | ZC3H13 | GSM4909286 | Human | Breast | IDC | 1.92e-05 | 1.12e-01 | 0.1081 |
| 23091 | ZC3H13 | GSM4909298 | Human | Breast | IDC | 1.89e-09 | 3.33e-01 | 0.1551 |
| 23091 | ZC3H13 | GSM4909311 | Human | Breast | IDC | 6.42e-11 | -1.47e-01 | 0.1534 |
| 23091 | ZC3H13 | GSM4909317 | Human | Breast | IDC | 7.82e-24 | 6.58e-01 | 0.1355 |
| 23091 | ZC3H13 | GSM4909319 | Human | Breast | IDC | 1.05e-12 | -1.10e-01 | 0.1563 |
| 23091 | ZC3H13 | GSM4909321 | Human | Breast | IDC | 1.45e-02 | -1.17e-02 | 0.1559 |
| 23091 | ZC3H13 | M2 | Human | Breast | IDC | 6.36e-10 | 7.79e-01 | 0.21 |
| 23091 | ZC3H13 | P1 | Human | Breast | IDC | 4.81e-02 | -9.76e-02 | 0.1527 |
| 23091 | ZC3H13 | DCIS2 | Human | Breast | DCIS | 3.07e-63 | 4.34e-01 | 0.0085 |
| 23091 | ZC3H13 | LZE4T | Human | Esophagus | ESCC | 9.91e-14 | 4.44e-01 | 0.0811 |
| 23091 | ZC3H13 | LZE5T | Human | Esophagus | ESCC | 7.45e-05 | 2.99e-01 | 0.0514 |
| 23091 | ZC3H13 | LZE7T | Human | Esophagus | ESCC | 2.77e-04 | 2.42e-01 | 0.0667 |
| 23091 | ZC3H13 | LZE8T | Human | Esophagus | ESCC | 4.13e-10 | 2.45e-01 | 0.067 |
| 23091 | ZC3H13 | LZE20T | Human | Esophagus | ESCC | 1.46e-02 | 9.89e-02 | 0.0662 |
| 23091 | ZC3H13 | LZE22D1 | Human | Esophagus | HGIN | 2.12e-02 | 2.16e-02 | 0.0595 |
| 23091 | ZC3H13 | LZE24T | Human | Esophagus | ESCC | 3.61e-18 | 2.44e-01 | 0.0596 |
| 23091 | ZC3H13 | LZE21T | Human | Esophagus | ESCC | 4.63e-03 | 1.81e-01 | 0.0655 |
| 23091 | ZC3H13 | LZE6T | Human | Esophagus | ESCC | 3.69e-04 | 3.08e-02 | 0.0845 |
| 23091 | ZC3H13 | P1T-E | Human | Esophagus | ESCC | 5.77e-05 | 5.96e-01 | 0.0875 |
| 23091 | ZC3H13 | P2T-E | Human | Esophagus | ESCC | 9.72e-32 | 6.46e-01 | 0.1177 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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. |
Top |
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:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
| GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
| GO:000838026 | Esophagus | HGIN | RNA splicing | 160/2587 | 434/18723 | 3.74e-34 | 1.12e-30 | 160 |
| GO:00198277 | Esophagus | HGIN | stem cell population maintenance | 39/2587 | 131/18723 | 1.63e-06 | 6.14e-05 | 39 |
| GO:00987278 | Esophagus | HGIN | maintenance of cell number | 39/2587 | 134/18723 | 3.02e-06 | 1.03e-04 | 39 |
| GO:20000362 | Esophagus | HGIN | regulation of stem cell population maintenance | 11/2587 | 33/18723 | 3.55e-03 | 3.26e-02 | 11 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:009872714 | Esophagus | ESCC | maintenance of cell number | 90/8552 | 134/18723 | 3.94e-07 | 5.43e-06 | 90 |
| GO:001982714 | Esophagus | ESCC | stem cell population maintenance | 88/8552 | 131/18723 | 5.23e-07 | 6.97e-06 | 88 |
| GO:00015101 | Esophagus | ESCC | RNA methylation | 58/8552 | 83/18723 | 6.87e-06 | 6.94e-05 | 58 |
| GO:00800092 | Esophagus | ESCC | mRNA methylation | 14/8552 | 16/18723 | 6.78e-04 | 3.56e-03 | 14 |
| GO:00165561 | Esophagus | ESCC | mRNA modification | 21/8552 | 27/18723 | 6.88e-04 | 3.61e-03 | 21 |
| GO:20000361 | Esophagus | ESCC | regulation of stem cell population maintenance | 23/8552 | 33/18723 | 4.57e-03 | 1.78e-02 | 23 |
| GO:00083807 | Liver | NAFLD | RNA splicing | 70/1882 | 434/18723 | 4.62e-05 | 1.10e-03 | 70 |
| GO:00198273 | Liver | NAFLD | stem cell population maintenance | 26/1882 | 131/18723 | 5.40e-04 | 7.38e-03 | 26 |
| GO:00987273 | Liver | NAFLD | maintenance of cell number | 26/1882 | 134/18723 | 7.72e-04 | 9.73e-03 | 26 |
| GO:0043414 | Liver | NAFLD | macromolecule methylation | 47/1882 | 316/18723 | 4.08e-03 | 3.41e-02 | 47 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| ZC3H13 | SNV | Missense_Mutation | c.2654N>A | p.Arg885Lys | p.R885K | Q5T200 | protein_coding | tolerated_low_confidence(0.51) | benign(0.003) | TCGA-A8-A08J-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| ZC3H13 | SNV | Missense_Mutation | novel | c.1882G>C | p.Glu628Gln | p.E628Q | Q5T200 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.703) | TCGA-AC-A6IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ZC3H13 | SNV | Missense_Mutation | rs375011338 | c.3782N>A | p.Arg1261Gln | p.R1261Q | Q5T200 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.992) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ZC3H13 | SNV | Missense_Mutation | rs767948149 | c.3259N>A | p.Ala1087Thr | p.A1087T | Q5T200 | protein_coding | tolerated_low_confidence(0.88) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ZC3H13 | SNV | Missense_Mutation | c.286N>T | p.Val96Leu | p.V96L | Q5T200 | protein_coding | deleterious_low_confidence(0.01) | benign(0.207) | TCGA-BH-A1ES-06 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| ZC3H13 | SNV | Missense_Mutation | rs550536100 | c.1988G>A | p.Arg663Gln | p.R663Q | Q5T200 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.988) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ZC3H13 | SNV | Missense_Mutation | c.58A>C | p.Thr20Pro | p.T20P | Q5T200 | protein_coding | tolerated_low_confidence(0.24) | possibly_damaging(0.69) | TCGA-GI-A2C8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Adriamycin | SD | |
| ZC3H13 | insertion | Nonsense_Mutation | novel | c.3337_3338insTCTCTTGAG | p.Thr1113delinsIleSerTerAla | p.T1113delinsIS*A | Q5T200 | protein_coding | TCGA-A8-A08T-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| ZC3H13 | insertion | In_Frame_Ins | novel | c.2009_2010insCAATGCAGCTGG | p.Asp670_Arg671insAsnAlaAlaGly | p.D670_R671insNAAG | Q5T200 | protein_coding | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ZC3H13 | insertion | In_Frame_Ins | novel | c.2196_2197insAAGCTTGGGCCTGTGAGTTGTCAT | p.Asp732_His733insLysLeuGlyProValSerCysHis | p.D732_H733insKLGPVSCH | Q5T200 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |