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Gene: CHPF2 |
Gene summary for CHPF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHPF2 | Gene ID | 54480 |
| Gene name | chondroitin polymerizing factor 2 | |
| Gene Alias | CSGLCA-T | |
| Cytomap | 7q36.1 | |
| Gene Type | protein-coding | GO ID | GO:0006022 | UniProtAcc | B3KPG6 |
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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 |
| 54480 | CHPF2 | LZE7T | Human | Esophagus | ESCC | 1.81e-02 | 2.30e-01 | 0.0667 |
| 54480 | CHPF2 | LZE20T | Human | Esophagus | ESCC | 1.06e-03 | 1.32e-01 | 0.0662 |
| 54480 | CHPF2 | LZE24T | Human | Esophagus | ESCC | 1.35e-04 | 1.10e-01 | 0.0596 |
| 54480 | CHPF2 | P1T-E | Human | Esophagus | ESCC | 1.72e-02 | 1.50e-01 | 0.0875 |
| 54480 | CHPF2 | P2T-E | Human | Esophagus | ESCC | 7.63e-08 | 8.96e-02 | 0.1177 |
| 54480 | CHPF2 | P4T-E | Human | Esophagus | ESCC | 2.10e-03 | 1.03e-01 | 0.1323 |
| 54480 | CHPF2 | P5T-E | Human | Esophagus | ESCC | 3.42e-04 | 4.96e-02 | 0.1327 |
| 54480 | CHPF2 | P8T-E | Human | Esophagus | ESCC | 3.80e-12 | 1.76e-01 | 0.0889 |
| 54480 | CHPF2 | P9T-E | Human | Esophagus | ESCC | 1.01e-07 | 1.54e-01 | 0.1131 |
| 54480 | CHPF2 | P10T-E | Human | Esophagus | ESCC | 3.87e-11 | 1.84e-01 | 0.116 |
| 54480 | CHPF2 | P11T-E | Human | Esophagus | ESCC | 7.61e-05 | 3.48e-01 | 0.1426 |
| 54480 | CHPF2 | P12T-E | Human | Esophagus | ESCC | 1.01e-12 | 2.41e-01 | 0.1122 |
| 54480 | CHPF2 | P15T-E | Human | Esophagus | ESCC | 1.20e-20 | 4.41e-01 | 0.1149 |
| 54480 | CHPF2 | P16T-E | Human | Esophagus | ESCC | 2.15e-10 | 1.17e-01 | 0.1153 |
| 54480 | CHPF2 | P19T-E | Human | Esophagus | ESCC | 9.63e-05 | 4.91e-01 | 0.1662 |
| 54480 | CHPF2 | P20T-E | Human | Esophagus | ESCC | 2.05e-03 | 3.43e-02 | 0.1124 |
| 54480 | CHPF2 | P21T-E | Human | Esophagus | ESCC | 4.01e-16 | 2.52e-01 | 0.1617 |
| 54480 | CHPF2 | P22T-E | Human | Esophagus | ESCC | 2.69e-04 | 5.69e-02 | 0.1236 |
| 54480 | CHPF2 | P24T-E | Human | Esophagus | ESCC | 1.77e-10 | 1.22e-01 | 0.1287 |
| 54480 | CHPF2 | P26T-E | Human | Esophagus | ESCC | 4.60e-05 | 1.24e-01 | 0.1276 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:00091002 | Esophagus | ESCC | glycoprotein metabolic process | 226/8552 | 387/18723 | 2.64e-07 | 3.94e-06 | 226 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:00442725 | Esophagus | ESCC | sulfur compound biosynthetic process | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| GO:00091012 | Esophagus | ESCC | glycoprotein biosynthetic process | 181/8552 | 317/18723 | 2.54e-05 | 2.15e-04 | 181 |
| GO:0006029 | Esophagus | ESCC | proteoglycan metabolic process | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
| GO:0030166 | Esophagus | ESCC | proteoglycan biosynthetic process | 35/8552 | 56/18723 | 8.30e-03 | 2.94e-02 | 35 |
| GO:0006024 | Esophagus | ESCC | glycosaminoglycan biosynthetic process | 45/8552 | 75/18723 | 8.75e-03 | 3.08e-02 | 45 |
| GO:0006023 | Esophagus | ESCC | aminoglycan biosynthetic process | 47/8552 | 79/18723 | 9.29e-03 | 3.23e-02 | 47 |
| GO:000679021 | Liver | HCC | sulfur compound metabolic process | 212/7958 | 339/18723 | 5.60e-14 | 3.39e-12 | 212 |
| GO:00442722 | Liver | HCC | sulfur compound biosynthetic process | 95/7958 | 148/18723 | 7.89e-08 | 1.58e-06 | 95 |
| GO:0009100 | Liver | HCC | glycoprotein metabolic process | 193/7958 | 387/18723 | 1.89e-03 | 9.62e-03 | 193 |
| GO:00442724 | Oral cavity | OSCC | sulfur compound biosynthetic process | 82/7305 | 148/18723 | 3.71e-05 | 3.31e-04 | 82 |
| GO:00067905 | Oral cavity | OSCC | sulfur compound metabolic process | 168/7305 | 339/18723 | 4.50e-05 | 3.84e-04 | 168 |
| GO:0030206 | Oral cavity | OSCC | chondroitin sulfate biosynthetic process | 15/7305 | 18/18723 | 1.53e-04 | 1.07e-03 | 15 |
| GO:00091001 | Oral cavity | OSCC | glycoprotein metabolic process | 185/7305 | 387/18723 | 2.37e-04 | 1.54e-03 | 185 |
| GO:00091011 | Oral cavity | OSCC | glycoprotein biosynthetic process | 151/7305 | 317/18723 | 1.01e-03 | 5.26e-03 | 151 |
| GO:0050650 | Oral cavity | OSCC | chondroitin sulfate proteoglycan biosynthetic process | 16/7305 | 23/18723 | 2.93e-03 | 1.27e-02 | 16 |
| GO:0030204 | Oral cavity | OSCC | chondroitin sulfate metabolic process | 19/7305 | 30/18723 | 6.03e-03 | 2.28e-02 | 19 |
| GO:000679012 | Oral cavity | LP | sulfur compound metabolic process | 106/4623 | 339/18723 | 3.36e-03 | 2.25e-02 | 106 |
| GO:00442726 | Thyroid | PTC | sulfur compound biosynthetic process | 63/5968 | 148/18723 | 3.91e-03 | 1.87e-02 | 63 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00532 | Oral cavity | OSCC | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 16/3704 | 21/8465 | 2.61e-03 | 6.77e-03 | 3.45e-03 | 16 |
| hsa005321 | Oral cavity | OSCC | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 16/3704 | 21/8465 | 2.61e-03 | 6.77e-03 | 3.45e-03 | 16 |
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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 |
| CHPF2 | SNV | Missense_Mutation | novel | c.908T>C | p.Phe303Ser | p.F303S | Q9P2E5 | protein_coding | deleterious(0.01) | possibly_damaging(0.599) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CHPF2 | SNV | Missense_Mutation | rs752470752 | c.464N>A | p.Arg155Gln | p.R155Q | Q9P2E5 | protein_coding | deleterious(0.01) | possibly_damaging(0.487) | TCGA-AA-3695-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CHPF2 | SNV | Missense_Mutation | rs374488900 | c.1693G>A | p.Ala565Thr | p.A565T | Q9P2E5 | protein_coding | deleterious(0) | benign(0.279) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHPF2 | SNV | Missense_Mutation | novel | c.1796N>A | p.Pro599His | p.P599H | Q9P2E5 | protein_coding | deleterious(0) | possibly_damaging(0.836) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHPF2 | SNV | Missense_Mutation | rs146697508 | c.2053C>T | p.Arg685Trp | p.R685W | Q9P2E5 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-CK-6748-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CHPF2 | SNV | Missense_Mutation | rs746382000 | c.1262N>A | p.Arg421His | p.R421H | Q9P2E5 | protein_coding | tolerated(0.54) | possibly_damaging(0.786) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| CHPF2 | SNV | Missense_Mutation | rs374488900 | c.1693G>A | p.Ala565Thr | p.A565T | Q9P2E5 | protein_coding | deleterious(0) | benign(0.279) | TCGA-F4-6461-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CHPF2 | SNV | Missense_Mutation | rs759727328 | c.1522N>A | p.Glu508Lys | p.E508K | Q9P2E5 | protein_coding | deleterious(0.01) | possibly_damaging(0.689) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| CHPF2 | insertion | Frame_Shift_Ins | novel | c.1536_1537insA | p.Asn513LysfsTer133 | p.N513Kfs*133 | Q9P2E5 | protein_coding | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| CHPF2 | SNV | Missense_Mutation | novel | c.532T>C | p.Phe178Leu | p.F178L | Q9P2E5 | protein_coding | deleterious(0) | possibly_damaging(0.804) | TCGA-A5-A0G1-01 | 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 |
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