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Gene: CPSF1 |
Gene summary for CPSF1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | CPSF1 | Gene ID | 29894 |
Gene name | cleavage and polyadenylation specific factor 1 | |
Gene Alias | CPSF160 | |
Cytomap | 8q24.3 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q10570 |
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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 |
29894 | CPSF1 | LZE4T | Human | Esophagus | ESCC | 2.77e-03 | 8.17e-02 | 0.0811 |
29894 | CPSF1 | LZE7T | Human | Esophagus | ESCC | 2.96e-10 | 5.52e-01 | 0.0667 |
29894 | CPSF1 | LZE20T | Human | Esophagus | ESCC | 3.61e-08 | 3.56e-01 | 0.0662 |
29894 | CPSF1 | LZE24T | Human | Esophagus | ESCC | 1.39e-07 | 2.11e-01 | 0.0596 |
29894 | CPSF1 | P1T-E | Human | Esophagus | ESCC | 1.74e-14 | 4.45e-01 | 0.0875 |
29894 | CPSF1 | P2T-E | Human | Esophagus | ESCC | 2.46e-14 | 2.66e-01 | 0.1177 |
29894 | CPSF1 | P4T-E | Human | Esophagus | ESCC | 1.35e-10 | 1.55e-01 | 0.1323 |
29894 | CPSF1 | P5T-E | Human | Esophagus | ESCC | 4.06e-12 | 1.57e-01 | 0.1327 |
29894 | CPSF1 | P8T-E | Human | Esophagus | ESCC | 3.21e-10 | 1.95e-01 | 0.0889 |
29894 | CPSF1 | P9T-E | Human | Esophagus | ESCC | 2.87e-09 | 1.41e-01 | 0.1131 |
29894 | CPSF1 | P10T-E | Human | Esophagus | ESCC | 5.83e-10 | 1.50e-01 | 0.116 |
29894 | CPSF1 | P11T-E | Human | Esophagus | ESCC | 4.28e-07 | 3.73e-01 | 0.1426 |
29894 | CPSF1 | P12T-E | Human | Esophagus | ESCC | 8.29e-24 | 4.17e-01 | 0.1122 |
29894 | CPSF1 | P15T-E | Human | Esophagus | ESCC | 1.52e-20 | 4.50e-01 | 0.1149 |
29894 | CPSF1 | P16T-E | Human | Esophagus | ESCC | 3.52e-19 | 3.06e-01 | 0.1153 |
29894 | CPSF1 | P17T-E | Human | Esophagus | ESCC | 3.21e-08 | 3.75e-01 | 0.1278 |
29894 | CPSF1 | P20T-E | Human | Esophagus | ESCC | 5.00e-16 | 1.99e-01 | 0.1124 |
29894 | CPSF1 | P21T-E | Human | Esophagus | ESCC | 2.92e-20 | 3.39e-01 | 0.1617 |
29894 | CPSF1 | P22T-E | Human | Esophagus | ESCC | 1.27e-12 | 1.92e-01 | 0.1236 |
29894 | CPSF1 | P23T-E | Human | Esophagus | ESCC | 4.37e-16 | 3.69e-01 | 0.108 |
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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:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
GO:003112412 | Esophagus | ESCC | mRNA 3'-end processing | 47/8552 | 62/18723 | 1.29e-06 | 1.58e-05 | 47 |
GO:00311233 | Esophagus | ESCC | RNA 3'-end processing | 76/8552 | 116/18723 | 1.25e-05 | 1.15e-04 | 76 |
GO:00063783 | Esophagus | ESCC | mRNA polyadenylation | 33/8552 | 44/18723 | 7.30e-05 | 5.49e-04 | 33 |
GO:00436313 | Esophagus | ESCC | RNA polyadenylation | 33/8552 | 45/18723 | 1.54e-04 | 1.02e-03 | 33 |
GO:00063793 | Esophagus | ESCC | mRNA cleavage | 17/8552 | 22/18723 | 2.60e-03 | 1.11e-02 | 17 |
GO:00987872 | Esophagus | ESCC | mRNA cleavage involved in mRNA processing | 11/8552 | 14/18723 | 1.30e-02 | 4.27e-02 | 11 |
GO:00311241 | Liver | HCC | mRNA 3'-end processing | 50/7958 | 62/18723 | 8.44e-10 | 2.60e-08 | 50 |
GO:00905011 | Liver | HCC | RNA phosphodiester bond hydrolysis | 101/7958 | 152/18723 | 1.99e-09 | 5.63e-08 | 101 |
GO:00311231 | Liver | HCC | RNA 3'-end processing | 81/7958 | 116/18723 | 2.27e-09 | 6.32e-08 | 81 |
GO:0090305 | Liver | HCC | nucleic acid phosphodiester bond hydrolysis | 152/7958 | 261/18723 | 1.90e-07 | 3.46e-06 | 152 |
GO:0006378 | Liver | HCC | mRNA polyadenylation | 35/7958 | 44/18723 | 5.70e-07 | 9.03e-06 | 35 |
GO:0043631 | Liver | HCC | RNA polyadenylation | 35/7958 | 45/18723 | 1.51e-06 | 2.15e-05 | 35 |
GO:0006379 | Liver | HCC | mRNA cleavage | 17/7958 | 22/18723 | 9.84e-04 | 5.70e-03 | 17 |
GO:0098789 | Liver | HCC | pre-mRNA cleavage required for polyadenylation | 11/7958 | 13/18723 | 2.38e-03 | 1.16e-02 | 11 |
GO:0098787 | Liver | HCC | mRNA cleavage involved in mRNA processing | 11/7958 | 14/18723 | 6.81e-03 | 2.73e-02 | 11 |
GO:00311242 | Oral cavity | OSCC | mRNA 3'-end processing | 49/7305 | 62/18723 | 1.40e-10 | 4.14e-09 | 49 |
GO:00905012 | Oral cavity | OSCC | RNA phosphodiester bond hydrolysis | 95/7305 | 152/18723 | 3.65e-09 | 8.22e-08 | 95 |
GO:00311232 | Oral cavity | OSCC | RNA 3'-end processing | 75/7305 | 116/18723 | 1.93e-08 | 3.79e-07 | 75 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0301521 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa0301531 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030158 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
hsa0301513 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
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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 |
CPSF1 | SNV | Missense_Mutation | novel | c.2432T>G | p.Phe811Cys | p.F811C | Q10570 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | rs782373256 | c.2803G>A | p.Glu935Lys | p.E935K | Q10570 | protein_coding | tolerated(0.41) | benign(0.086) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | novel | c.3884N>A | p.Arg1295His | p.R1295H | Q10570 | protein_coding | deleterious(0.05) | possibly_damaging(0.534) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | novel | c.3285N>T | p.Gln1095His | p.Q1095H | Q10570 | protein_coding | deleterious(0) | benign(0.409) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | rs782625053 | c.2956N>A | p.Gly986Ser | p.G986S | Q10570 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | rs782391720 | c.1699N>A | p.Asp567Asn | p.D567N | Q10570 | protein_coding | tolerated(0.21) | benign(0.013) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | rs782071262 | c.1618G>A | p.Ala540Thr | p.A540T | Q10570 | protein_coding | tolerated(0.14) | benign(0.166) | TCGA-AP-A05N-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CPSF1 | SNV | Missense_Mutation | rs763605694 | c.2288N>A | p.Arg763Gln | p.R763Q | Q10570 | protein_coding | tolerated(0.37) | benign(0.001) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
CPSF1 | SNV | Missense_Mutation | rs782071262 | c.1618N>A | p.Ala540Thr | p.A540T | Q10570 | protein_coding | tolerated(0.14) | benign(0.166) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
CPSF1 | SNV | Missense_Mutation | novel | c.2090C>T | p.Thr697Met | p.T697M | Q10570 | protein_coding | deleterious(0.03) | benign(0.205) | TCGA-AP-A1DV-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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