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Gene: ATF3 |
Gene summary for ATF3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ATF3 | Gene ID | 467 |
Gene name | activating transcription factor 3 | |
Gene Alias | ATF3 | |
Cytomap | 1q32.3 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | P18847 |
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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 |
467 | ATF3 | GSM5353222_PA_PB2B_Pool_1_3_S52_L002 | Human | Prostate | Tumor | 1.34e-04 | 5.33e-01 | 0.1608 |
467 | ATF3 | GSM5353224_PA_PR5186_Pool_1_2_3_S27_L001 | Human | Prostate | Tumor | 5.47e-24 | 1.07e+00 | 0.1621 |
467 | ATF3 | GSM5353225_PA_PR5196-1_Pool_1_2_3_S53_L002 | Human | Prostate | Tumor | 1.02e-02 | 7.24e-01 | 0.1619 |
467 | ATF3 | GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002 | Human | Prostate | Tumor | 3.43e-14 | 8.41e-01 | 0.1602 |
467 | ATF3 | GSM5353240_PA_PR5254_T1_S15_L001 | Human | Prostate | Tumor | 3.06e-27 | 9.34e-01 | 0.1575 |
467 | ATF3 | GSM5353243_PA_PR5261_T1_S23_L002 | Human | Prostate | Tumor | 1.60e-53 | 1.15e+00 | 0.1545 |
467 | ATF3 | GSM5353244_PA_PR5261_T2_S24_L002 | Human | Prostate | Tumor | 2.43e-42 | 1.14e+00 | 0.1569 |
467 | ATF3 | P1_S1_AK | Human | Skin | AK | 5.79e-38 | 7.92e-01 | -0.3399 |
467 | ATF3 | P2_S3_AK | Human | Skin | AK | 1.11e-57 | 9.20e-01 | -0.3287 |
467 | ATF3 | P2_S4_SCCIS | Human | Skin | SCCIS | 5.04e-13 | 5.14e-01 | -0.3043 |
467 | ATF3 | P3_S6_AK | Human | Skin | AK | 3.81e-22 | 6.61e-01 | -0.3256 |
467 | ATF3 | P4_S8_cSCC | Human | Skin | cSCC | 1.52e-30 | 9.19e-01 | -0.3095 |
467 | ATF3 | P5_S10_cSCC | Human | Skin | cSCC | 5.21e-71 | 1.04e+00 | -0.299 |
467 | ATF3 | P1_cSCC | Human | Skin | cSCC | 3.99e-05 | 1.02e+00 | 0.0292 |
467 | ATF3 | P2_cSCC | Human | Skin | cSCC | 1.39e-37 | 2.14e+00 | -0.024 |
467 | ATF3 | P4_cSCC | Human | Skin | cSCC | 1.46e-35 | 1.52e+00 | -0.00290000000000005 |
467 | ATF3 | P10_cSCC | Human | Skin | cSCC | 9.06e-04 | 7.04e-01 | 0.1017 |
467 | ATF3 | cSCC_p1 | Human | Skin | cSCC | 5.10e-03 | 1.28e-01 | -0.1916 |
467 | ATF3 | cSCC_p10 | Human | Skin | cSCC | 3.26e-02 | 1.14e-01 | -0.2095 |
467 | ATF3 | cSCC_p11 | Human | Skin | cSCC | 6.24e-04 | 8.73e-02 | -0.2102 |
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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:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
GO:00069869 | Breast | Precancer | response to unfolded protein | 28/1080 | 137/18723 | 3.81e-09 | 3.00e-07 | 28 |
GO:00359669 | Breast | Precancer | response to topologically incorrect protein | 29/1080 | 159/18723 | 3.00e-08 | 1.89e-06 | 29 |
GO:00349769 | Breast | Precancer | response to endoplasmic reticulum stress | 38/1080 | 256/18723 | 7.89e-08 | 4.60e-06 | 38 |
GO:00346209 | Breast | Precancer | cellular response to unfolded protein | 21/1080 | 96/18723 | 9.80e-08 | 5.46e-06 | 21 |
GO:20012356 | Breast | Precancer | positive regulation of apoptotic signaling pathway | 24/1080 | 126/18723 | 1.98e-07 | 1.01e-05 | 24 |
GO:00359679 | Breast | Precancer | cellular response to topologically incorrect protein | 22/1080 | 116/18723 | 6.84e-07 | 2.80e-05 | 22 |
GO:20012369 | Breast | Precancer | regulation of extrinsic apoptotic signaling pathway | 24/1080 | 151/18723 | 5.78e-06 | 1.70e-04 | 24 |
GO:00436209 | Breast | Precancer | regulation of DNA-templated transcription in response to stress | 13/1080 | 53/18723 | 7.06e-06 | 1.95e-04 | 13 |
GO:00971919 | Breast | Precancer | extrinsic apoptotic signaling pathway | 30/1080 | 219/18723 | 9.42e-06 | 2.50e-04 | 30 |
GO:00436189 | Breast | Precancer | regulation of transcription from RNA polymerase II promoter in response to stress | 12/1080 | 47/18723 | 1.02e-05 | 2.67e-04 | 12 |
GO:00309687 | Breast | Precancer | endoplasmic reticulum unfolded protein response | 15/1080 | 74/18723 | 1.74e-05 | 4.17e-04 | 15 |
GO:00712435 | Breast | Precancer | cellular response to arsenic-containing substance | 7/1080 | 20/18723 | 8.31e-05 | 1.61e-03 | 7 |
GO:00316679 | Breast | Precancer | response to nutrient levels | 47/1080 | 474/18723 | 2.09e-04 | 3.27e-03 | 47 |
GO:00714969 | Breast | Precancer | cellular response to external stimulus | 33/1080 | 320/18723 | 9.01e-04 | 1.03e-02 | 33 |
GO:00060066 | Breast | Precancer | glucose metabolic process | 23/1080 | 196/18723 | 9.54e-04 | 1.07e-02 | 23 |
GO:00316688 | Breast | Precancer | cellular response to extracellular stimulus | 27/1080 | 246/18723 | 1.02e-03 | 1.13e-02 | 27 |
GO:0035914 | Breast | Precancer | skeletal muscle cell differentiation | 11/1080 | 67/18723 | 1.47e-03 | 1.52e-02 | 11 |
GO:00092677 | Breast | Precancer | cellular response to starvation | 19/1080 | 156/18723 | 1.65e-03 | 1.67e-02 | 19 |
GO:19020418 | Breast | Precancer | regulation of extrinsic apoptotic signaling pathway via death domain receptors | 9/1080 | 49/18723 | 1.74e-03 | 1.74e-02 | 9 |
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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 |
ATF3 | DUCT1 | Pancreas | PanIN | FOSB,PPP1R15A,SERTAD1, etc. | 2.91e-01 |
∗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 |
ATF3 | SNV | Missense_Mutation | c.379G>A | p.Glu127Lys | p.E127K | P18847 | protein_coding | deleterious(0.05) | benign(0.247) | TCGA-A8-A09M-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | CR | |
ATF3 | SNV | Missense_Mutation | c.498N>C | p.Glu166Asp | p.E166D | P18847 | protein_coding | deleterious(0.01) | probably_damaging(0.967) | TCGA-AR-A1AN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
ATF3 | SNV | Missense_Mutation | c.62N>G | p.Pro21Arg | p.P21R | P18847 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
ATF3 | SNV | Missense_Mutation | novel | c.278G>A | p.Arg93Gln | p.R93Q | P18847 | protein_coding | tolerated(0.08) | possibly_damaging(0.634) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ATF3 | SNV | Missense_Mutation | novel | c.455C>T | p.Thr152Met | p.T152M | P18847 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ATF3 | SNV | Missense_Mutation | c.377C>T | p.Ala126Val | p.A126V | P18847 | protein_coding | tolerated(0.13) | benign(0.175) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
ATF3 | SNV | Missense_Mutation | novel | c.278G>A | p.Arg93Gln | p.R93Q | P18847 | protein_coding | tolerated(0.08) | possibly_damaging(0.634) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
ATF3 | SNV | Missense_Mutation | novel | c.284G>T | p.Arg95Ile | p.R95I | P18847 | protein_coding | deleterious(0) | possibly_damaging(0.848) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ATF3 | SNV | Missense_Mutation | novel | c.540N>T | p.Gln180His | p.Q180H | P18847 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.867) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
ATF3 | SNV | Missense_Mutation | c.505C>A | p.Leu169Ile | p.L169I | P18847 | protein_coding | tolerated(0.32) | probably_damaging(0.987) | TCGA-A5-A0GB-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 |
467 | ATF3 | TRANSCRIPTION FACTOR | PROGESTERONE | PROGESTERONE | 15674352 |
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