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Gene: RAD9A |
Gene summary for RAD9A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RAD9A | Gene ID | 5883 |
| Gene name | RAD9 checkpoint clamp component A | |
| Gene Alias | RAD9 | |
| Cytomap | 11q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | Q99638 |
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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 |
| 5883 | RAD9A | CCI_1 | Human | Cervix | CC | 2.60e-06 | 6.41e-01 | 0.528 |
| 5883 | RAD9A | CCI_2 | Human | Cervix | CC | 1.18e-06 | 5.64e-01 | 0.5249 |
| 5883 | RAD9A | CCI_3 | Human | Cervix | CC | 1.28e-02 | 3.35e-01 | 0.516 |
| 5883 | RAD9A | CCII_1 | Human | Cervix | CC | 1.11e-12 | 4.46e-01 | 0.3249 |
| 5883 | RAD9A | sample3 | Human | Cervix | CC | 1.06e-03 | 1.64e-01 | 0.1387 |
| 5883 | RAD9A | LZE2T | Human | Esophagus | ESCC | 1.15e-02 | 4.60e-01 | 0.082 |
| 5883 | RAD9A | LZE4T | Human | Esophagus | ESCC | 1.09e-10 | 2.54e-01 | 0.0811 |
| 5883 | RAD9A | LZE7T | Human | Esophagus | ESCC | 2.52e-05 | 3.76e-01 | 0.0667 |
| 5883 | RAD9A | LZE20T | Human | Esophagus | ESCC | 1.76e-10 | 3.82e-01 | 0.0662 |
| 5883 | RAD9A | LZE22D1 | Human | Esophagus | HGIN | 9.00e-05 | 2.19e-01 | 0.0595 |
| 5883 | RAD9A | LZE22T | Human | Esophagus | ESCC | 1.13e-03 | 3.08e-01 | 0.068 |
| 5883 | RAD9A | LZE24T | Human | Esophagus | ESCC | 8.46e-14 | 4.36e-01 | 0.0596 |
| 5883 | RAD9A | LZE6T | Human | Esophagus | ESCC | 1.16e-02 | 2.42e-01 | 0.0845 |
| 5883 | RAD9A | P1T-E | Human | Esophagus | ESCC | 7.08e-14 | 6.70e-01 | 0.0875 |
| 5883 | RAD9A | P2T-E | Human | Esophagus | ESCC | 5.39e-29 | 6.13e-01 | 0.1177 |
| 5883 | RAD9A | P4T-E | Human | Esophagus | ESCC | 1.65e-27 | 6.23e-01 | 0.1323 |
| 5883 | RAD9A | P5T-E | Human | Esophagus | ESCC | 4.21e-19 | 4.69e-01 | 0.1327 |
| 5883 | RAD9A | P8T-E | Human | Esophagus | ESCC | 4.76e-37 | 8.74e-01 | 0.0889 |
| 5883 | RAD9A | P9T-E | Human | Esophagus | ESCC | 1.85e-12 | 2.60e-01 | 0.1131 |
| 5883 | RAD9A | P10T-E | Human | Esophagus | ESCC | 5.00e-18 | 2.79e-01 | 0.116 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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. |
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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:19019878 | Thyroid | PTC | regulation of cell cycle phase transition | 167/5968 | 390/18723 | 2.97e-06 | 3.87e-05 | 167 |
| GO:004277010 | Thyroid | PTC | signal transduction in response to DNA damage | 81/5968 | 172/18723 | 2.07e-05 | 2.08e-04 | 81 |
| GO:00459307 | Thyroid | PTC | negative regulation of mitotic cell cycle | 105/5968 | 235/18723 | 2.41e-05 | 2.39e-04 | 105 |
| GO:00109486 | Thyroid | PTC | negative regulation of cell cycle process | 122/5968 | 294/18723 | 2.94e-04 | 2.08e-03 | 122 |
| GO:19019885 | Thyroid | PTC | negative regulation of cell cycle phase transition | 104/5968 | 249/18723 | 6.01e-04 | 3.82e-03 | 104 |
| GO:00070936 | Thyroid | PTC | mitotic cell cycle checkpoint | 58/5968 | 129/18723 | 1.22e-03 | 6.97e-03 | 58 |
| GO:00000756 | Thyroid | PTC | cell cycle checkpoint | 72/5968 | 169/18723 | 2.09e-03 | 1.11e-02 | 72 |
| GO:00903055 | Thyroid | PTC | nucleic acid phosphodiester bond hydrolysis | 105/5968 | 261/18723 | 2.53e-03 | 1.31e-02 | 105 |
| GO:00000777 | Thyroid | PTC | DNA damage checkpoint | 50/5968 | 115/18723 | 5.79e-03 | 2.61e-02 | 50 |
| GO:00447736 | Thyroid | PTC | mitotic DNA damage checkpoint | 37/5968 | 81/18723 | 6.35e-03 | 2.79e-02 | 37 |
| GO:00447746 | Thyroid | PTC | mitotic DNA integrity checkpoint | 38/5968 | 85/18723 | 8.78e-03 | 3.66e-02 | 38 |
| GO:000734622 | Thyroid | ATC | regulation of mitotic cell cycle | 236/6293 | 457/18723 | 7.58e-16 | 5.92e-14 | 236 |
| GO:007121427 | Thyroid | ATC | cellular response to abiotic stimulus | 169/6293 | 331/18723 | 3.24e-11 | 1.08e-09 | 169 |
| GO:010400427 | Thyroid | ATC | cellular response to environmental stimulus | 169/6293 | 331/18723 | 3.24e-11 | 1.08e-09 | 169 |
| GO:190198715 | Thyroid | ATC | regulation of cell cycle phase transition | 187/6293 | 390/18723 | 2.36e-09 | 5.61e-08 | 187 |
| GO:007147825 | Thyroid | ATC | cellular response to radiation | 101/6293 | 186/18723 | 4.67e-09 | 1.04e-07 | 101 |
| GO:000931426 | Thyroid | ATC | response to radiation | 210/6293 | 456/18723 | 1.69e-08 | 3.39e-07 | 210 |
| GO:004578614 | Thyroid | ATC | negative regulation of cell cycle | 181/6293 | 385/18723 | 2.64e-08 | 5.07e-07 | 181 |
| GO:0010212110 | Thyroid | ATC | response to ionizing radiation | 82/6293 | 148/18723 | 3.88e-08 | 7.15e-07 | 82 |
| GO:007147927 | Thyroid | ATC | cellular response to ionizing radiation | 46/6293 | 72/18723 | 1.41e-07 | 2.30e-06 | 46 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0421810 | Cervix | CC | Cellular senescence | 49/1267 | 156/8465 | 1.30e-07 | 1.63e-06 | 9.61e-07 | 49 |
| hsa0421815 | Cervix | CC | Cellular senescence | 49/1267 | 156/8465 | 1.30e-07 | 1.63e-06 | 9.61e-07 | 49 |
| hsa0421828 | Esophagus | HGIN | Cellular senescence | 42/1383 | 156/8465 | 4.94e-04 | 5.03e-03 | 4.00e-03 | 42 |
| hsa04218111 | Esophagus | HGIN | Cellular senescence | 42/1383 | 156/8465 | 4.94e-04 | 5.03e-03 | 4.00e-03 | 42 |
| hsa0421829 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
| hsa0421838 | Esophagus | ESCC | Cellular senescence | 119/4205 | 156/8465 | 5.89e-12 | 9.40e-11 | 4.81e-11 | 119 |
| hsa042188 | Lung | IAC | Cellular senescence | 40/1053 | 156/8465 | 4.44e-06 | 1.44e-04 | 9.59e-05 | 40 |
| hsa0421813 | Lung | IAC | Cellular senescence | 40/1053 | 156/8465 | 4.44e-06 | 1.44e-04 | 9.59e-05 | 40 |
| hsa0421843 | Lung | MIAC | Cellular senescence | 22/507 | 156/8465 | 1.43e-04 | 3.46e-03 | 2.50e-03 | 22 |
| hsa0421853 | Lung | MIAC | Cellular senescence | 22/507 | 156/8465 | 1.43e-04 | 3.46e-03 | 2.50e-03 | 22 |
| hsa0421820 | Oral cavity | OSCC | Cellular senescence | 112/3704 | 156/8465 | 8.04e-13 | 1.42e-11 | 7.21e-12 | 112 |
| hsa04218110 | Oral cavity | OSCC | Cellular senescence | 112/3704 | 156/8465 | 8.04e-13 | 1.42e-11 | 7.21e-12 | 112 |
| hsa0421827 | Oral cavity | LP | Cellular senescence | 71/2418 | 156/8465 | 4.17e-06 | 3.75e-05 | 2.42e-05 | 71 |
| hsa0421837 | Oral cavity | LP | Cellular senescence | 71/2418 | 156/8465 | 4.17e-06 | 3.75e-05 | 2.42e-05 | 71 |
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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 |
| RAD9A | SNV | Missense_Mutation | novel | c.797C>T | p.Ser266Leu | p.S266L | Q99638 | protein_coding | tolerated(0.19) | benign(0.003) | TCGA-LD-A74U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | taxotere | SD |
| RAD9A | deletion | Frame_Shift_Del | novel | c.1083delN | p.Arg362AlafsTer35 | p.R362Afs*35 | Q99638 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RAD9A | SNV | Missense_Mutation | novel | c.231N>A | p.Met77Ile | p.M77I | Q99638 | protein_coding | tolerated(0.36) | benign(0.015) | TCGA-MA-AA3Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RAD9A | SNV | Missense_Mutation | c.677N>G | p.Leu226Arg | p.L226R | Q99638 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AA-3511-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| RAD9A | SNV | Missense_Mutation | novel | c.527N>C | p.Val176Ala | p.V176A | Q99638 | protein_coding | tolerated(0.06) | probably_damaging(0.969) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD |
| RAD9A | deletion | Frame_Shift_Del | c.1124delN | p.Gln377ArgfsTer20 | p.Q377Rfs*20 | Q99638 | protein_coding | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |||
| RAD9A | SNV | Missense_Mutation | novel | c.793N>A | p.Leu265Ile | p.L265I | Q99638 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RAD9A | SNV | Missense_Mutation | rs377299831 | c.215N>A | p.Arg72His | p.R72H | Q99638 | protein_coding | tolerated(0.14) | benign(0.03) | TCGA-A5-A2K7-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | taxol | SD |
| RAD9A | SNV | Missense_Mutation | rs569583450 | c.403N>A | p.Val135Ile | p.V135I | Q99638 | protein_coding | tolerated(0.13) | benign(0.123) | TCGA-AJ-A3BG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| RAD9A | SNV | Missense_Mutation | novel | c.778N>C | p.Phe260Leu | p.F260L | Q99638 | protein_coding | tolerated(0.28) | benign(0.057) | TCGA-AX-A3FT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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