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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 | GSM4909286 | Human | Breast | IDC | 1.49e-24 | -7.65e-01 | 0.1081 |
467 | ATF3 | GSM4909290 | Human | Breast | IDC | 2.98e-23 | -8.38e-01 | 0.2096 |
467 | ATF3 | GSM4909291 | Human | Breast | IDC | 1.97e-02 | 3.39e-01 | 0.1753 |
467 | ATF3 | GSM4909294 | Human | Breast | IDC | 3.37e-12 | -5.57e-01 | 0.2022 |
467 | ATF3 | GSM4909296 | Human | Breast | IDC | 6.67e-04 | -3.38e-01 | 0.1524 |
467 | ATF3 | GSM4909297 | Human | Breast | IDC | 1.36e-07 | -3.22e-01 | 0.1517 |
467 | ATF3 | GSM4909298 | Human | Breast | IDC | 2.00e-12 | -6.42e-01 | 0.1551 |
467 | ATF3 | GSM4909299 | Human | Breast | IDC | 2.53e-15 | 5.34e-01 | 0.035 |
467 | ATF3 | GSM4909300 | Human | Breast | IDC | 8.60e-15 | 6.96e-01 | 0.0334 |
467 | ATF3 | GSM4909304 | Human | Breast | IDC | 1.61e-09 | -6.29e-01 | 0.1636 |
467 | ATF3 | GSM4909307 | Human | Breast | IDC | 2.56e-15 | -6.75e-01 | 0.1569 |
467 | ATF3 | GSM4909311 | Human | Breast | IDC | 3.52e-22 | -5.71e-01 | 0.1534 |
467 | ATF3 | GSM4909312 | Human | Breast | IDC | 1.10e-08 | -5.08e-01 | 0.1552 |
467 | ATF3 | GSM4909315 | Human | Breast | IDC | 3.05e-02 | -3.53e-01 | 0.21 |
467 | ATF3 | GSM4909316 | Human | Breast | IDC | 3.65e-05 | -7.07e-01 | 0.21 |
467 | ATF3 | GSM4909317 | Human | Breast | IDC | 8.47e-06 | 3.95e-01 | 0.1355 |
467 | ATF3 | GSM4909319 | Human | Breast | IDC | 1.28e-25 | -1.55e-01 | 0.1563 |
467 | ATF3 | GSM4909321 | Human | Breast | IDC | 6.04e-26 | 5.66e-01 | 0.1559 |
467 | ATF3 | brca1 | Human | Breast | Precancer | 3.13e-04 | -5.07e-01 | -0.0338 |
467 | ATF3 | brca2 | Human | Breast | Precancer | 2.53e-07 | -6.06e-01 | -0.024 |
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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:0008625111 | Thyroid | ATC | extrinsic apoptotic signaling pathway via death domain receptors | 50/6293 | 82/18723 | 3.47e-07 | 5.13e-06 | 50 |
GO:006053724 | Thyroid | ATC | muscle tissue development | 181/6293 | 403/18723 | 1.27e-06 | 1.62e-05 | 181 |
GO:0043620210 | Thyroid | ATC | regulation of DNA-templated transcription in response to stress | 35/6293 | 53/18723 | 1.39e-06 | 1.74e-05 | 35 |
GO:004361829 | Thyroid | ATC | regulation of transcription from RNA polymerase II promoter in response to stress | 32/6293 | 47/18723 | 1.42e-06 | 1.77e-05 | 32 |
GO:003009933 | Thyroid | ATC | myeloid cell differentiation | 170/6293 | 381/18723 | 4.26e-06 | 4.68e-05 | 170 |
GO:004668523 | Thyroid | ATC | response to arsenic-containing substance | 24/6293 | 33/18723 | 4.98e-06 | 5.40e-05 | 24 |
GO:1902041110 | Thyroid | ATC | regulation of extrinsic apoptotic signaling pathway via death domain receptors | 32/6293 | 49/18723 | 5.63e-06 | 6.00e-05 | 32 |
GO:001931814 | Thyroid | ATC | hexose metabolic process | 111/6293 | 237/18723 | 1.51e-05 | 1.41e-04 | 111 |
GO:001470622 | Thyroid | ATC | striated muscle tissue development | 168/6293 | 384/18723 | 1.91e-05 | 1.73e-04 | 168 |
GO:000599615 | Thyroid | ATC | monosaccharide metabolic process | 118/6293 | 257/18723 | 2.56e-05 | 2.20e-04 | 118 |
GO:007124323 | Thyroid | ATC | cellular response to arsenic-containing substance | 16/6293 | 20/18723 | 2.79e-05 | 2.36e-04 | 16 |
GO:000600616 | Thyroid | ATC | glucose metabolic process | 93/6293 | 196/18723 | 3.85e-05 | 3.14e-04 | 93 |
GO:003600323 | Thyroid | ATC | positive regulation of transcription from RNA polymerase II promoter in response to stress | 17/6293 | 24/18723 | 2.14e-04 | 1.41e-03 | 17 |
GO:190204316 | Thyroid | ATC | positive regulation of extrinsic apoptotic signaling pathway via death domain receptors | 11/6293 | 13/18723 | 2.30e-04 | 1.49e-03 | 11 |
GO:000751716 | Thyroid | ATC | muscle organ development | 139/6293 | 327/18723 | 4.45e-04 | 2.64e-03 | 139 |
GO:004340926 | Thyroid | ATC | negative regulation of MAPK cascade | 82/6293 | 180/18723 | 5.51e-04 | 3.19e-03 | 82 |
GO:199092813 | Thyroid | ATC | response to amino acid starvation | 28/6293 | 49/18723 | 6.01e-04 | 3.43e-03 | 28 |
GO:199044021 | Thyroid | ATC | positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress | 9/6293 | 11/18723 | 1.46e-03 | 7.47e-03 | 9 |
GO:003419813 | Thyroid | ATC | cellular response to amino acid starvation | 25/6293 | 46/18723 | 3.00e-03 | 1.36e-02 | 25 |
GO:004636411 | Thyroid | ATC | monosaccharide biosynthetic process | 39/6293 | 82/18723 | 6.04e-03 | 2.42e-02 | 39 |
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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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