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Gene: R3HDML |
Gene summary for R3HDML |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | R3HDML | Gene ID | 140902 |
| Gene name | R3H domain containing like | |
| Gene Alias | dJ881L22.3 | |
| Cytomap | 20q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q9H3Y0 |
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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 |
| 140902 | R3HDML | HTA11_347_2000001011 | Human | Colorectum | AD | 8.62e-06 | 2.98e-01 | -0.1954 |
| 140902 | R3HDML | HTA11_696_2000001011 | Human | Colorectum | AD | 9.59e-03 | 2.07e-01 | -0.1464 |
| 140902 | R3HDML | HTA11_866_2000001011 | Human | Colorectum | AD | 8.73e-03 | 1.81e-01 | -0.1001 |
| 140902 | R3HDML | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.74e-14 | 6.05e-01 | 0.3859 |
| 140902 | R3HDML | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.63e-15 | 5.04e-01 | 0.3005 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0052547 | Colorectum | AD | regulation of peptidase activity | 137/3918 | 461/18723 | 4.12e-06 | 1.12e-04 | 137 |
| GO:0045861 | Colorectum | AD | negative regulation of proteolysis | 106/3918 | 351/18723 | 2.33e-05 | 4.57e-04 | 106 |
| GO:00525472 | Colorectum | MSS | regulation of peptidase activity | 130/3467 | 461/18723 | 1.81e-07 | 8.13e-06 | 130 |
| GO:00458612 | Colorectum | MSS | negative regulation of proteolysis | 97/3467 | 351/18723 | 1.57e-05 | 3.54e-04 | 97 |
| GO:00513461 | Colorectum | MSS | negative regulation of hydrolase activity | 92/3467 | 379/18723 | 2.85e-03 | 2.22e-02 | 92 |
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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 |
| 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. |
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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 |
| R3HDML | SNV | Missense_Mutation | c.188N>A | p.Met63Lys | p.M63K | Q9H3Y0 | protein_coding | tolerated(0.33) | benign(0.368) | TCGA-A2-A1G6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| R3HDML | SNV | Missense_Mutation | rs777264582 | c.221N>A | p.Arg74Gln | p.R74Q | Q9H3Y0 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B6-A0I2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| R3HDML | SNV | Missense_Mutation | rs373660156 | c.535N>T | p.Arg179Trp | p.R179W | Q9H3Y0 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C5-A8XJ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
| R3HDML | SNV | Missense_Mutation | c.660N>C | p.Lys220Asn | p.K220N | Q9H3Y0 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR | |
| R3HDML | SNV | Missense_Mutation | c.161N>A | p.Arg54Gln | p.R54Q | Q9H3Y0 | protein_coding | tolerated(0.32) | benign(0.031) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| R3HDML | SNV | Missense_Mutation | c.493N>G | p.Thr165Ala | p.T165A | Q9H3Y0 | protein_coding | deleterious(0.02) | benign(0) | TCGA-AA-A00O-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| R3HDML | SNV | Missense_Mutation | novel | c.4N>T | p.Pro2Ser | p.P2S | Q9H3Y0 | protein_coding | tolerated(0.43) | benign(0.001) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| R3HDML | SNV | Missense_Mutation | novel | c.296N>T | p.Ala99Val | p.A99V | Q9H3Y0 | protein_coding | deleterious(0.02) | probably_damaging(0.947) | TCGA-AJ-A3NH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR |
| R3HDML | SNV | Missense_Mutation | novel | c.257N>G | p.Tyr86Cys | p.Y86C | Q9H3Y0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A1DM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| R3HDML | SNV | Missense_Mutation | rs766996028 | c.212N>G | p.Asn71Ser | p.N71S | Q9H3Y0 | protein_coding | deleterious(0.01) | possibly_damaging(0.759) | TCGA-AX-A2HJ-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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