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Gene: RECQL4 |
Gene summary for RECQL4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RECQL4 | Gene ID | 9401 |
| Gene name | RecQ like helicase 4 | |
| Gene Alias | RECQ4 | |
| Cytomap | 8q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000723 | UniProtAcc | O94761 |
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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 |
| 9401 | RECQL4 | P2T-E | Human | Esophagus | ESCC | 1.66e-02 | 1.27e-01 | 0.1177 |
| 9401 | RECQL4 | P5T-E | Human | Esophagus | ESCC | 2.02e-06 | 1.32e-01 | 0.1327 |
| 9401 | RECQL4 | P8T-E | Human | Esophagus | ESCC | 1.88e-11 | 2.90e-01 | 0.0889 |
| 9401 | RECQL4 | P9T-E | Human | Esophagus | ESCC | 8.38e-03 | 1.03e-01 | 0.1131 |
| 9401 | RECQL4 | P10T-E | Human | Esophagus | ESCC | 7.90e-03 | 8.28e-02 | 0.116 |
| 9401 | RECQL4 | P16T-E | Human | Esophagus | ESCC | 4.31e-06 | 1.18e-01 | 0.1153 |
| 9401 | RECQL4 | P17T-E | Human | Esophagus | ESCC | 4.79e-04 | 2.33e-01 | 0.1278 |
| 9401 | RECQL4 | P21T-E | Human | Esophagus | ESCC | 1.88e-04 | 1.31e-01 | 0.1617 |
| 9401 | RECQL4 | P24T-E | Human | Esophagus | ESCC | 1.66e-02 | 9.07e-02 | 0.1287 |
| 9401 | RECQL4 | P26T-E | Human | Esophagus | ESCC | 4.12e-11 | 3.19e-01 | 0.1276 |
| 9401 | RECQL4 | P27T-E | Human | Esophagus | ESCC | 3.97e-04 | 1.46e-01 | 0.1055 |
| 9401 | RECQL4 | P28T-E | Human | Esophagus | ESCC | 9.35e-10 | 2.22e-01 | 0.1149 |
| 9401 | RECQL4 | P31T-E | Human | Esophagus | ESCC | 1.78e-03 | 1.22e-01 | 0.1251 |
| 9401 | RECQL4 | P32T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.18e-01 | 0.1666 |
| 9401 | RECQL4 | P37T-E | Human | Esophagus | ESCC | 2.88e-04 | 1.19e-01 | 0.1371 |
| 9401 | RECQL4 | P52T-E | Human | Esophagus | ESCC | 7.98e-13 | 2.18e-01 | 0.1555 |
| 9401 | RECQL4 | P54T-E | Human | Esophagus | ESCC | 1.28e-04 | 1.79e-01 | 0.0975 |
| 9401 | RECQL4 | P74T-E | Human | Esophagus | ESCC | 2.69e-06 | 2.14e-01 | 0.1479 |
| 9401 | RECQL4 | P75T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.45e-01 | 0.1125 |
| 9401 | RECQL4 | P79T-E | Human | Esophagus | ESCC | 7.90e-03 | 1.02e-01 | 0.1154 |
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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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:000072319 | Esophagus | ESCC | telomere maintenance | 99/8552 | 131/18723 | 2.68e-12 | 1.08e-10 | 99 |
| GO:00062612 | Esophagus | ESCC | DNA-dependent DNA replication | 100/8552 | 151/18723 | 2.61e-07 | 3.94e-06 | 100 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:003239214 | Esophagus | ESCC | DNA geometric change | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:003250813 | Esophagus | ESCC | DNA duplex unwinding | 58/8552 | 84/18723 | 1.23e-05 | 1.14e-04 | 58 |
| GO:003220014 | Esophagus | ESCC | telomere organization | 99/8552 | 159/18723 | 1.77e-05 | 1.57e-04 | 99 |
| GO:00063101 | Esophagus | ESCC | DNA recombination | 168/8552 | 305/18723 | 5.58e-04 | 3.05e-03 | 168 |
| GO:00007241 | Esophagus | ESCC | double-strand break repair via homologous recombination | 79/8552 | 138/18723 | 4.05e-03 | 1.62e-02 | 79 |
| GO:00007251 | Esophagus | ESCC | recombinational repair | 80/8552 | 140/18723 | 4.10e-03 | 1.63e-02 | 80 |
| GO:000072311 | Liver | HCC | telomere maintenance | 85/7958 | 131/18723 | 1.86e-07 | 3.40e-06 | 85 |
| GO:00062601 | Liver | HCC | DNA replication | 146/7958 | 260/18723 | 5.68e-06 | 7.02e-05 | 146 |
| GO:003239211 | Liver | HCC | DNA geometric change | 54/7958 | 90/18723 | 6.04e-04 | 3.79e-03 | 54 |
| GO:00063021 | Liver | HCC | double-strand break repair | 131/7958 | 251/18723 | 1.17e-03 | 6.54e-03 | 131 |
| GO:00322001 | Liver | HCC | telomere organization | 86/7958 | 159/18723 | 2.06e-03 | 1.04e-02 | 86 |
| GO:00325081 | Liver | HCC | DNA duplex unwinding | 49/7958 | 84/18723 | 2.46e-03 | 1.19e-02 | 49 |
| GO:0006261 | Liver | HCC | DNA-dependent DNA replication | 80/7958 | 151/18723 | 5.91e-03 | 2.44e-02 | 80 |
| GO:00062603 | Oral cavity | OSCC | DNA replication | 159/7305 | 260/18723 | 3.25e-13 | 1.59e-11 | 159 |
| GO:000072316 | Oral cavity | OSCC | telomere maintenance | 85/7305 | 131/18723 | 1.72e-09 | 4.09e-08 | 85 |
| GO:00323925 | Oral cavity | OSCC | DNA geometric change | 59/7305 | 90/18723 | 3.03e-07 | 4.63e-06 | 59 |
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| 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 |
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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 |
| RECQL4 | SNV | Missense_Mutation | novel | c.478N>T | p.Pro160Ser | p.P160S | protein_coding | tolerated(0.22) | benign(0.068) | TCGA-A7-A425-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | adriamycin | PD | |
| RECQL4 | SNV | Missense_Mutation | novel | c.3331N>C | p.Glu1111Gln | p.E1111Q | protein_coding | deleterious(0.04) | possibly_damaging(0.908) | TCGA-C8-A275-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RECQL4 | SNV | Missense_Mutation | novel | c.1394N>G | p.Thr465Arg | p.T465R | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-UL-AAZ6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | herceptin | SD | |
| RECQL4 | SNV | Missense_Mutation | novel | c.2849N>T | p.Pro950Leu | p.P950L | protein_coding | tolerated(0.39) | benign(0.105) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RECQL4 | SNV | Missense_Mutation | novel | c.2275N>T | p.Ala759Ser | p.A759S | protein_coding | tolerated(0.37) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RECQL4 | SNV | Missense_Mutation | c.264N>T | p.Lys88Asn | p.K88N | protein_coding | tolerated(0.14) | benign(0.038) | TCGA-C5-A3HE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | ||
| RECQL4 | SNV | Missense_Mutation | rs755425093 | c.1664N>T | p.Ser555Leu | p.S555L | protein_coding | deleterious(0) | possibly_damaging(0.668) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RECQL4 | SNV | Missense_Mutation | novel | c.2590C>G | p.Gln864Glu | p.Q864E | protein_coding | tolerated(0.32) | benign(0.012) | TCGA-LP-A4AW-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RECQL4 | SNV | Missense_Mutation | c.3343G>C | p.Glu1115Gln | p.E1115Q | protein_coding | tolerated(0.34) | benign(0.009) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| RECQL4 | SNV | Missense_Mutation | novel | c.1420N>C | p.Glu474Gln | p.E474Q | protein_coding | tolerated(0.19) | benign(0.062) | TCGA-VS-A953-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | 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 |
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