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Gene: CCL25 |
Gene summary for CCL25 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CCL25 | Gene ID | 6370 |
| Gene name | C-C motif chemokine ligand 25 | |
| Gene Alias | Ck beta-15 | |
| Cytomap | 19p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | O15444 |
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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 |
| 6370 | CCL25 | Pat01-B | Human | Stomach | GC | 2.03e-18 | 4.61e-01 | 0.5754 |
| 6370 | CCL25 | Pat03-B | Human | Stomach | GC | 7.83e-16 | 3.83e-01 | 0.3693 |
| 6370 | CCL25 | Pat17-B | Human | Stomach | GC | 1.87e-04 | 1.89e-01 | 0.3109 |
| 6370 | CCL25 | SIM_1 | Human | Stomach | SIM | 3.11e-14 | 4.80e-01 | 0.3573 |
| 6370 | CCL25 | SIM_4 | Human | Stomach | SIM | 4.19e-06 | 2.99e-01 | 0.2664 |
| 6370 | CCL25 | EGC | Human | Stomach | GC | 3.97e-04 | 2.06e-01 | 0.1683 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia |
| ∗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:00457856 | Stomach | GC | positive regulation of cell adhesion | 56/1159 | 437/18723 | 1.79e-07 | 1.02e-05 | 56 |
| GO:00224076 | Stomach | GC | regulation of cell-cell adhesion | 55/1159 | 448/18723 | 9.21e-07 | 4.39e-05 | 55 |
| GO:0071356 | Stomach | GC | cellular response to tumor necrosis factor | 34/1159 | 229/18723 | 1.85e-06 | 8.24e-05 | 34 |
| GO:0034612 | Stomach | GC | response to tumor necrosis factor | 35/1159 | 253/18723 | 6.68e-06 | 2.54e-04 | 35 |
| GO:0071621 | Stomach | GC | granulocyte chemotaxis | 22/1159 | 125/18723 | 7.88e-06 | 2.80e-04 | 22 |
| GO:0007159 | Stomach | GC | leukocyte cell-cell adhesion | 45/1159 | 371/18723 | 1.21e-05 | 3.99e-04 | 45 |
| GO:0030595 | Stomach | GC | leukocyte chemotaxis | 32/1159 | 230/18723 | 1.45e-05 | 4.68e-04 | 32 |
| GO:0050900 | Stomach | GC | leukocyte migration | 44/1159 | 369/18723 | 2.30e-05 | 6.81e-04 | 44 |
| GO:0097530 | Stomach | GC | granulocyte migration | 23/1159 | 148/18723 | 3.99e-05 | 1.00e-03 | 23 |
| GO:1903037 | Stomach | GC | regulation of leukocyte cell-cell adhesion | 40/1159 | 336/18723 | 5.53e-05 | 1.30e-03 | 40 |
| GO:0030593 | Stomach | GC | neutrophil chemotaxis | 18/1159 | 103/18723 | 5.67e-05 | 1.31e-03 | 18 |
| GO:0097529 | Stomach | GC | myeloid leukocyte migration | 29/1159 | 220/18723 | 9.69e-05 | 1.97e-03 | 29 |
| GO:0002685 | Stomach | GC | regulation of leukocyte migration | 28/1159 | 210/18723 | 1.04e-04 | 2.05e-03 | 28 |
| GO:0002683 | Stomach | GC | negative regulation of immune system process | 47/1159 | 434/18723 | 1.36e-04 | 2.52e-03 | 47 |
| GO:1990266 | Stomach | GC | neutrophil migration | 19/1159 | 122/18723 | 1.77e-04 | 3.08e-03 | 19 |
| GO:00108106 | Stomach | GC | regulation of cell-substrate adhesion | 28/1159 | 221/18723 | 2.49e-04 | 4.17e-03 | 28 |
| GO:00315895 | Stomach | GC | cell-substrate adhesion | 40/1159 | 363/18723 | 2.91e-04 | 4.68e-03 | 40 |
| GO:0060326 | Stomach | GC | cell chemotaxis | 35/1159 | 310/18723 | 4.34e-04 | 6.46e-03 | 35 |
| GO:00108116 | Stomach | GC | positive regulation of cell-substrate adhesion | 18/1159 | 123/18723 | 5.62e-04 | 7.81e-03 | 18 |
| GO:0071674 | Stomach | GC | mononuclear cell migration | 24/1159 | 196/18723 | 1.08e-03 | 1.27e-02 | 24 |
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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 |
| CCL25 | SNV | Missense_Mutation | c.334N>T | p.His112Tyr | p.H112Y | O15444 | protein_coding | tolerated(1) | benign(0.094) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| CCL25 | SNV | Missense_Mutation | novel | c.345N>T | p.Lys115Asn | p.K115N | O15444 | protein_coding | tolerated(0.22) | benign(0.036) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCL25 | SNV | Missense_Mutation | novel | c.422N>T | p.Ser141Phe | p.S141F | O15444 | protein_coding | deleterious(0) | possibly_damaging(0.588) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CCL25 | SNV | Missense_Mutation | novel | c.290T>G | p.Phe97Cys | p.F97C | O15444 | protein_coding | tolerated(0.18) | benign(0.001) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| CCL25 | SNV | Missense_Mutation | novel | c.292N>A | p.Ala98Thr | p.A98T | O15444 | protein_coding | tolerated(0.52) | benign(0.027) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CCL25 | SNV | Missense_Mutation | novel | c.418N>A | p.Val140Ile | p.V140I | O15444 | protein_coding | deleterious(0.02) | benign(0) | TCGA-AJ-A3OJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| CCL25 | SNV | Missense_Mutation | novel | c.227N>A | p.Gly76Glu | p.G76E | O15444 | protein_coding | deleterious(0.01) | probably_damaging(0.977) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCL25 | SNV | Missense_Mutation | rs750634500 | c.136N>A | p.Ala46Thr | p.A46T | O15444 | protein_coding | tolerated(0.11) | benign(0.239) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CCL25 | SNV | Missense_Mutation | c.325N>T | p.Ala109Ser | p.A109S | O15444 | protein_coding | tolerated(0.78) | benign(0) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| CCL25 | SNV | Missense_Mutation | c.254G>T | p.Arg85Ile | p.R85I | O15444 | protein_coding | tolerated(0.23) | benign(0.006) | TCGA-BK-A6W3-01 | 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 |
| 6370 | CCL25 | HORMONE ACTIVITY, DRUGGABLE GENOME | TNF-ALPHA | 15492285 |
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