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Gene: CARF |
Gene summary for CARF |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CARF | Gene ID | 79800 |
| Gene name | calcium responsive transcription factor | |
| Gene Alias | ALS2CR8 | |
| Cytomap | 2q33.2 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | A0A024R427 |
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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 |
| 79800 | CARF | NAFLD1 | Human | Liver | NAFLD | 2.18e-02 | 4.00e-01 | -0.04 |
| 79800 | CARF | HCC1_Meng | Human | Liver | HCC | 1.33e-08 | -4.77e-02 | 0.0246 |
| 79800 | CARF | HCC2_Meng | Human | Liver | HCC | 1.34e-05 | 1.77e-02 | 0.0107 |
| 79800 | CARF | HCC1 | Human | Liver | HCC | 5.05e-12 | 2.96e+00 | 0.5336 |
| 79800 | CARF | HCC2 | Human | Liver | HCC | 1.02e-15 | 2.08e+00 | 0.5341 |
| 79800 | CARF | HCC5 | Human | Liver | HCC | 2.34e-08 | 1.68e+00 | 0.4932 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00100387 | Liver | NAFLD | response to metal ion | 62/1882 | 373/18723 | 5.05e-05 | 1.19e-03 | 62 |
| GO:00515923 | Liver | NAFLD | response to calcium ion | 26/1882 | 149/18723 | 3.69e-03 | 3.15e-02 | 26 |
| GO:001003822 | Liver | HCC | response to metal ion | 208/7958 | 373/18723 | 1.35e-07 | 2.56e-06 | 208 |
| GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
| GO:007124112 | Liver | HCC | cellular response to inorganic substance | 119/7958 | 226/18723 | 1.26e-03 | 6.92e-03 | 119 |
| GO:005159221 | Liver | HCC | response to calcium ion | 81/7958 | 149/18723 | 2.26e-03 | 1.13e-02 | 81 |
| GO:007124812 | Liver | HCC | cellular response to metal ion | 101/7958 | 197/18723 | 7.82e-03 | 3.10e-02 | 101 |
| GO:19015221 | Liver | HCC | positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus | 15/7958 | 22/18723 | 1.35e-02 | 4.80e-02 | 15 |
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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 |
| CARF | SNV | Missense_Mutation | c.1065N>C | p.Lys355Asn | p.K355N | Q8N187 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| CARF | SNV | Missense_Mutation | c.2107N>C | p.Glu703Gln | p.E703Q | Q8N187 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.961) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| CARF | SNV | Missense_Mutation | c.679N>C | p.Glu227Gln | p.E227Q | Q8N187 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CARF | SNV | Missense_Mutation | c.710N>G | p.His237Arg | p.H237R | Q8N187 | protein_coding | deleterious(0) | possibly_damaging(0.773) | TCGA-B6-A0X1-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| CARF | SNV | Missense_Mutation | rs762792094 | c.2158A>G | p.Lys720Glu | p.K720E | Q8N187 | protein_coding | deleterious_low_confidence(0.04) | benign(0.003) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CARF | deletion | Frame_Shift_Del | novel | c.1155delC | p.Cys386AlafsTer36 | p.C386Afs*36 | Q8N187 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CARF | SNV | Missense_Mutation | c.734N>C | p.Trp245Ser | p.W245S | Q8N187 | protein_coding | deleterious(0.03) | benign(0.344) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| CARF | SNV | Missense_Mutation | c.82C>G | p.Leu28Val | p.L28V | Q8N187 | protein_coding | tolerated_low_confidence(0.07) | benign(0.025) | TCGA-EK-A2R7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CARF | SNV | Missense_Mutation | novel | c.1958A>T | p.Asp653Val | p.D653V | Q8N187 | protein_coding | deleterious_low_confidence(0.01) | benign(0.241) | TCGA-VS-A8EJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| CARF | SNV | Missense_Mutation | rs200547023 | c.953N>A | p.Arg318Gln | p.R318Q | Q8N187 | protein_coding | deleterious(0.01) | possibly_damaging(0.743) | TCGA-VS-A8Q8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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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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