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Gene: CLCF1 |
Gene summary for CLCF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CLCF1 | Gene ID | 23529 |
| Gene name | cardiotrophin like cytokine factor 1 | |
| Gene Alias | BSF-3 | |
| Cytomap | 11q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | Q9UBD9 |
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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 |
| 23529 | CLCF1 | LZE24T | Human | Esophagus | ESCC | 2.90e-03 | 3.30e-01 | 0.0596 |
| 23529 | CLCF1 | P4T-E | Human | Esophagus | ESCC | 3.51e-04 | 2.55e-01 | 0.1323 |
| 23529 | CLCF1 | P8T-E | Human | Esophagus | ESCC | 2.19e-30 | 1.06e+00 | 0.0889 |
| 23529 | CLCF1 | P9T-E | Human | Esophagus | ESCC | 6.59e-04 | 2.82e-01 | 0.1131 |
| 23529 | CLCF1 | P10T-E | Human | Esophagus | ESCC | 5.31e-04 | 6.49e-02 | 0.116 |
| 23529 | CLCF1 | P12T-E | Human | Esophagus | ESCC | 6.81e-13 | 4.80e-01 | 0.1122 |
| 23529 | CLCF1 | P15T-E | Human | Esophagus | ESCC | 1.20e-04 | 7.84e-02 | 0.1149 |
| 23529 | CLCF1 | P16T-E | Human | Esophagus | ESCC | 3.34e-04 | -3.76e-02 | 0.1153 |
| 23529 | CLCF1 | P21T-E | Human | Esophagus | ESCC | 7.91e-09 | 4.10e-01 | 0.1617 |
| 23529 | CLCF1 | P22T-E | Human | Esophagus | ESCC | 5.31e-03 | -3.09e-03 | 0.1236 |
| 23529 | CLCF1 | P23T-E | Human | Esophagus | ESCC | 2.87e-05 | 5.41e-01 | 0.108 |
| 23529 | CLCF1 | P24T-E | Human | Esophagus | ESCC | 2.17e-09 | 2.73e-01 | 0.1287 |
| 23529 | CLCF1 | P31T-E | Human | Esophagus | ESCC | 3.45e-04 | 2.53e-01 | 0.1251 |
| 23529 | CLCF1 | P32T-E | Human | Esophagus | ESCC | 9.98e-08 | 1.24e-01 | 0.1666 |
| 23529 | CLCF1 | P36T-E | Human | Esophagus | ESCC | 1.00e-06 | 5.75e-01 | 0.1187 |
| 23529 | CLCF1 | P37T-E | Human | Esophagus | ESCC | 2.94e-10 | 2.46e-01 | 0.1371 |
| 23529 | CLCF1 | P42T-E | Human | Esophagus | ESCC | 9.21e-03 | 2.93e-01 | 0.1175 |
| 23529 | CLCF1 | P47T-E | Human | Esophagus | ESCC | 1.75e-10 | 3.15e-01 | 0.1067 |
| 23529 | CLCF1 | P49T-E | Human | Esophagus | ESCC | 1.85e-12 | 2.35e+00 | 0.1768 |
| 23529 | CLCF1 | P54T-E | Human | Esophagus | ESCC | 6.65e-20 | 8.15e-01 | 0.0975 |
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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 | ||
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00466517 | Oral cavity | OSCC | lymphocyte proliferation | 131/7305 | 288/18723 | 1.41e-02 | 4.67e-02 | 131 |
| GO:00022002 | Oral cavity | OSCC | somatic diversification of immune receptors | 40/7305 | 77/18723 | 1.42e-02 | 4.69e-02 | 40 |
| GO:0002562 | Oral cavity | OSCC | somatic diversification of immune receptors via germline recombination within a single locus | 35/7305 | 66/18723 | 1.43e-02 | 4.69e-02 | 35 |
| GO:0016444 | Oral cavity | OSCC | somatic cell DNA recombination | 35/7305 | 66/18723 | 1.43e-02 | 4.69e-02 | 35 |
| GO:00706657 | Oral cavity | OSCC | positive regulation of leukocyte proliferation | 72/7305 | 150/18723 | 1.53e-02 | 4.95e-02 | 72 |
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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 |
| CLCF1 | SNV | Missense_Mutation | rs764602656 | c.322G>A | p.Glu108Lys | p.E108K | Q9UBD9 | protein_coding | tolerated(0.98) | benign(0.007) | TCGA-D8-A27R-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin+cyclophosphamide | SD |
| CLCF1 | SNV | Missense_Mutation | rs761887384 | c.364N>T | p.Arg122Cys | p.R122C | Q9UBD9 | protein_coding | deleterious(0.05) | possibly_damaging(0.566) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CLCF1 | SNV | Missense_Mutation | c.172N>A | p.Ala58Thr | p.A58T | Q9UBD9 | protein_coding | tolerated(0.15) | possibly_damaging(0.616) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
| CLCF1 | SNV | Missense_Mutation | rs757544375 | c.550N>A | p.Asp184Asn | p.D184N | Q9UBD9 | protein_coding | tolerated(0.05) | benign(0.124) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CLCF1 | SNV | Missense_Mutation | novel | c.50N>T | p.Thr17Met | p.T17M | Q9UBD9 | protein_coding | deleterious(0.02) | benign(0.09) | TCGA-D1-A2G0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CLCF1 | SNV | Missense_Mutation | novel | c.68C>T | p.Pro23Leu | p.P23L | Q9UBD9 | protein_coding | deleterious(0.01) | possibly_damaging(0.559) | TCGA-DD-AACH-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| CLCF1 | SNV | Missense_Mutation | c.463G>A | p.Gly155Ser | p.G155S | Q9UBD9 | protein_coding | tolerated(0.06) | probably_damaging(0.986) | TCGA-BR-4357-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| CLCF1 | SNV | Missense_Mutation | c.146N>G | p.Tyr49Cys | p.Y49C | Q9UBD9 | protein_coding | deleterious(0) | benign(0.021) | TCGA-BR-8059-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| CLCF1 | SNV | Missense_Mutation | novel | c.377C>T | p.Thr126Ile | p.T126I | Q9UBD9 | protein_coding | tolerated(0.24) | benign(0.046) | TCGA-D7-A6EY-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| CLCF1 | SNV | Missense_Mutation | novel | c.566N>G | p.Lys189Arg | p.K189R | Q9UBD9 | protein_coding | tolerated(1) | benign(0.096) | TCGA-VQ-A91K-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | CR |
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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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