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Gene: CHAF1A |
Gene summary for CHAF1A |
Gene summary. |
Gene information | Species | Human | Gene symbol | CHAF1A | Gene ID | 10036 |
Gene name | chromatin assembly factor 1 subunit A | |
Gene Alias | CAF-1 | |
Cytomap | 19p13.3 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q13111 |
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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 |
10036 | CHAF1A | LZE7T | Human | Esophagus | ESCC | 9.32e-08 | 3.53e-01 | 0.0667 |
10036 | CHAF1A | LZE24T | Human | Esophagus | ESCC | 7.65e-05 | 1.35e-01 | 0.0596 |
10036 | CHAF1A | LZE21T | Human | Esophagus | ESCC | 1.16e-05 | 2.85e-01 | 0.0655 |
10036 | CHAF1A | P1T-E | Human | Esophagus | ESCC | 1.98e-11 | 6.14e-01 | 0.0875 |
10036 | CHAF1A | P2T-E | Human | Esophagus | ESCC | 3.99e-22 | 4.38e-01 | 0.1177 |
10036 | CHAF1A | P4T-E | Human | Esophagus | ESCC | 3.52e-15 | 3.95e-01 | 0.1323 |
10036 | CHAF1A | P5T-E | Human | Esophagus | ESCC | 1.00e-14 | 2.77e-01 | 0.1327 |
10036 | CHAF1A | P8T-E | Human | Esophagus | ESCC | 2.78e-07 | 2.43e-01 | 0.0889 |
10036 | CHAF1A | P9T-E | Human | Esophagus | ESCC | 2.41e-06 | 2.13e-01 | 0.1131 |
10036 | CHAF1A | P10T-E | Human | Esophagus | ESCC | 7.30e-12 | 3.07e-01 | 0.116 |
10036 | CHAF1A | P15T-E | Human | Esophagus | ESCC | 2.11e-03 | 1.26e-01 | 0.1149 |
10036 | CHAF1A | P16T-E | Human | Esophagus | ESCC | 6.19e-03 | 1.29e-01 | 0.1153 |
10036 | CHAF1A | P17T-E | Human | Esophagus | ESCC | 8.50e-05 | 2.24e-01 | 0.1278 |
10036 | CHAF1A | P20T-E | Human | Esophagus | ESCC | 6.20e-06 | 1.51e-01 | 0.1124 |
10036 | CHAF1A | P21T-E | Human | Esophagus | ESCC | 2.73e-04 | 1.09e-01 | 0.1617 |
10036 | CHAF1A | P22T-E | Human | Esophagus | ESCC | 2.41e-03 | 1.34e-01 | 0.1236 |
10036 | CHAF1A | P23T-E | Human | Esophagus | ESCC | 5.52e-07 | 2.00e-01 | 0.108 |
10036 | CHAF1A | P24T-E | Human | Esophagus | ESCC | 2.61e-06 | 2.71e-01 | 0.1287 |
10036 | CHAF1A | P26T-E | Human | Esophagus | ESCC | 8.56e-05 | 1.89e-01 | 0.1276 |
10036 | CHAF1A | P27T-E | Human | Esophagus | ESCC | 7.19e-05 | 1.59e-01 | 0.1055 |
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Transcriptomic changes along malignancy continuum. |
∗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:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
GO:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
GO:00062603 | Oral cavity | OSCC | DNA replication | 159/7305 | 260/18723 | 3.25e-13 | 1.59e-11 | 159 |
GO:000632510 | Oral cavity | OSCC | chromatin organization | 190/7305 | 409/18723 | 1.17e-03 | 5.97e-03 | 190 |
GO:000632520 | Thyroid | PTC | chromatin organization | 183/5968 | 409/18723 | 2.55e-08 | 5.70e-07 | 183 |
GO:00062606 | Thyroid | PTC | DNA replication | 114/5968 | 260/18723 | 3.09e-05 | 2.95e-04 | 114 |
GO:00063385 | Thyroid | PTC | chromatin remodeling | 106/5968 | 255/18723 | 6.56e-04 | 4.13e-03 | 106 |
GO:0006325110 | Thyroid | ATC | chromatin organization | 189/6293 | 409/18723 | 6.40e-08 | 1.13e-06 | 189 |
GO:000626013 | Thyroid | ATC | DNA replication | 124/6293 | 260/18723 | 1.58e-06 | 1.93e-05 | 124 |
GO:000633813 | Thyroid | ATC | chromatin remodeling | 109/6293 | 255/18723 | 1.38e-03 | 7.15e-03 | 109 |
GO:00718242 | Thyroid | ATC | protein-DNA complex subunit organization | 103/6293 | 241/18723 | 1.84e-03 | 9.03e-03 | 103 |
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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 |
CHAF1A | SNV | Missense_Mutation | rs573779621 | c.1288N>T | p.Arg430Trp | p.R430W | Q13111 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
CHAF1A | SNV | Missense_Mutation | c.432N>T | p.Arg144Ser | p.R144S | Q13111 | protein_coding | tolerated_low_confidence(0.71) | benign(0.003) | TCGA-F4-6703-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHAF1A | SNV | Missense_Mutation | novel | c.1169N>T | p.Arg390Leu | p.R390L | Q13111 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-F4-6806-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | irinotecan | PD |
CHAF1A | SNV | Missense_Mutation | c.2189N>T | p.Arg730Met | p.R730M | Q13111 | protein_coding | deleterious(0.03) | probably_damaging(0.946) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHAF1A | SNV | Missense_Mutation | rs775109223 | c.319N>A | p.Glu107Lys | p.E107K | Q13111 | protein_coding | tolerated(1) | benign(0) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
CHAF1A | SNV | Missense_Mutation | c.2006N>G | p.Asp669Gly | p.D669G | Q13111 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHAF1A | SNV | Missense_Mutation | novel | c.896N>A | p.Pro299Gln | p.P299Q | Q13111 | protein_coding | tolerated(1) | benign(0.007) | TCGA-AG-A02G-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | PD |
CHAF1A | SNV | Missense_Mutation | novel | c.1027C>T | p.Arg343Cys | p.R343C | Q13111 | protein_coding | deleterious(0) | possibly_damaging(0.855) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
CHAF1A | deletion | Frame_Shift_Del | c.1370delN | p.Lys459ArgfsTer51 | p.K459Rfs*51 | Q13111 | protein_coding | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |||
CHAF1A | deletion | Frame_Shift_Del | novel | c.1456delN | p.Ala486LeufsTer24 | p.A486Lfs*24 | Q13111 | protein_coding | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | 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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