|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: ID4 |
Gene summary for ID4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ID4 | Gene ID | 3400 |
| Gene name | inhibitor of DNA binding 4, HLH protein | |
| Gene Alias | IDB4 | |
| Cytomap | 6p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | P47928 |
Top |
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 |
| 3400 | ID4 | CA_HPV_1 | Human | Cervix | CC | 8.11e-04 | -1.67e-01 | 0.0264 |
| 3400 | ID4 | CA_HPV_3 | Human | Cervix | CC | 3.20e-18 | 4.95e-01 | 0.0414 |
| 3400 | ID4 | H2 | Human | Cervix | HSIL_HPV | 2.34e-02 | 2.42e-01 | 0.0632 |
| 3400 | ID4 | T2 | Human | Cervix | CC | 3.81e-03 | 5.24e-01 | 0.0709 |
| 3400 | ID4 | AEH-subject1 | Human | Endometrium | AEH | 2.59e-04 | 2.67e-01 | -0.3059 |
| 3400 | ID4 | AEH-subject3 | Human | Endometrium | AEH | 2.59e-07 | 3.13e-01 | -0.2576 |
| 3400 | ID4 | AEH-subject4 | Human | Endometrium | AEH | 7.72e-03 | -7.15e-02 | -0.2657 |
| 3400 | ID4 | AEH-subject5 | Human | Endometrium | AEH | 3.51e-19 | -4.77e-01 | -0.2953 |
| 3400 | ID4 | EEC-subject1 | Human | Endometrium | EEC | 1.78e-04 | -1.62e-01 | -0.2682 |
| 3400 | ID4 | EEC-subject2 | Human | Endometrium | EEC | 1.85e-04 | -2.34e-01 | -0.2607 |
| 3400 | ID4 | EEC-subject3 | Human | Endometrium | EEC | 2.90e-22 | -3.83e-01 | -0.2525 |
| 3400 | ID4 | GSM5276934 | Human | Endometrium | EEC | 8.10e-22 | -4.82e-01 | -0.0913 |
| 3400 | ID4 | GSM5276937 | Human | Endometrium | EEC | 2.42e-16 | -5.08e-01 | -0.0897 |
| 3400 | ID4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.49e-17 | -2.73e-01 | -0.1869 |
| 3400 | ID4 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.53e-22 | -2.42e-01 | -0.1875 |
| 3400 | ID4 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.73e-19 | -1.16e-01 | -0.1883 |
| 3400 | ID4 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 6.56e-18 | -2.89e-01 | -0.1934 |
| 3400 | ID4 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 8.80e-32 | -2.53e-01 | -0.1917 |
| 3400 | ID4 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 8.85e-30 | -3.83e-01 | -0.1916 |
| 3400 | ID4 | LZE24T | Human | Esophagus | ESCC | 1.25e-02 | 9.50e-03 | 0.0596 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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. |
Top |
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:00180223 | Lung | IAC | peptidyl-lysine methylation | 27/2061 | 131/18723 | 9.41e-04 | 1.14e-02 | 27 |
| GO:00064794 | Lung | IAC | protein methylation | 34/2061 | 181/18723 | 1.28e-03 | 1.45e-02 | 34 |
| GO:00082134 | Lung | IAC | protein alkylation | 34/2061 | 181/18723 | 1.28e-03 | 1.45e-02 | 34 |
| GO:00165714 | Lung | IAC | histone methylation | 28/2061 | 141/18723 | 1.39e-03 | 1.53e-02 | 28 |
| GO:0061647 | Lung | IAC | histone H3-K9 modification | 12/2061 | 48/18723 | 4.87e-03 | 3.77e-02 | 12 |
| GO:00515671 | Lung | IAC | histone H3-K9 methylation | 10/2061 | 37/18723 | 5.45e-03 | 4.08e-02 | 10 |
| GO:000206413 | Lung | AIS | epithelial cell development | 48/1849 | 220/18723 | 1.06e-07 | 1.18e-05 | 48 |
| GO:001657012 | Lung | AIS | histone modification | 81/1849 | 463/18723 | 2.30e-07 | 2.16e-05 | 81 |
| GO:003410113 | Lung | AIS | erythrocyte homeostasis | 30/1849 | 129/18723 | 6.51e-06 | 2.92e-04 | 30 |
| GO:003021813 | Lung | AIS | erythrocyte differentiation | 28/1849 | 120/18723 | 1.22e-05 | 4.71e-04 | 28 |
| GO:006145812 | Lung | AIS | reproductive system development | 70/1849 | 427/18723 | 1.52e-05 | 5.50e-04 | 70 |
| GO:004860811 | Lung | AIS | reproductive structure development | 69/1849 | 424/18723 | 2.23e-05 | 7.42e-04 | 69 |
| GO:003009913 | Lung | AIS | myeloid cell differentiation | 63/1849 | 381/18723 | 3.05e-05 | 9.70e-04 | 63 |
| GO:000226213 | Lung | AIS | myeloid cell homeostasis | 32/1849 | 157/18723 | 5.57e-05 | 1.57e-03 | 32 |
| GO:004887213 | Lung | AIS | homeostasis of number of cells | 47/1849 | 272/18723 | 1.03e-04 | 2.50e-03 | 47 |
| GO:000632512 | Lung | AIS | chromatin organization | 62/1849 | 409/18723 | 4.24e-04 | 7.29e-03 | 62 |
| GO:003496811 | Lung | AIS | histone lysine methylation | 22/1849 | 115/18723 | 1.82e-03 | 2.05e-02 | 22 |
| GO:001657111 | Lung | AIS | histone methylation | 25/1849 | 141/18723 | 2.78e-03 | 2.77e-02 | 25 |
| GO:001802211 | Lung | AIS | peptidyl-lysine methylation | 23/1849 | 131/18723 | 4.54e-03 | 4.00e-02 | 23 |
| GO:000647911 | Lung | AIS | protein methylation | 29/1849 | 181/18723 | 6.16e-03 | 4.98e-02 | 29 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa043504 | Endometrium | AEH | TGF-beta signaling pathway | 26/1197 | 108/8465 | 3.82e-03 | 2.18e-02 | 1.59e-02 | 26 |
| hsa0435011 | Endometrium | AEH | TGF-beta signaling pathway | 26/1197 | 108/8465 | 3.82e-03 | 2.18e-02 | 1.59e-02 | 26 |
| hsa043502 | Endometrium | EEC | TGF-beta signaling pathway | 26/1237 | 108/8465 | 5.95e-03 | 3.12e-02 | 2.33e-02 | 26 |
| hsa043503 | Endometrium | EEC | TGF-beta signaling pathway | 26/1237 | 108/8465 | 5.95e-03 | 3.12e-02 | 2.33e-02 | 26 |
| hsa043507 | Esophagus | ESCC | TGF-beta signaling pathway | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa0435014 | Esophagus | ESCC | TGF-beta signaling pathway | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa043506 | Oral cavity | OSCC | TGF-beta signaling pathway | 60/3704 | 108/8465 | 8.66e-03 | 1.97e-02 | 1.00e-02 | 60 |
| hsa0435013 | Oral cavity | OSCC | TGF-beta signaling pathway | 60/3704 | 108/8465 | 8.66e-03 | 1.97e-02 | 1.00e-02 | 60 |
| hsa0435041 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
| hsa0435051 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
| hsa043505 | Prostate | BPH | TGF-beta signaling pathway | 35/1718 | 108/8465 | 1.98e-03 | 7.92e-03 | 4.90e-03 | 35 |
| hsa0435012 | Prostate | BPH | TGF-beta signaling pathway | 35/1718 | 108/8465 | 1.98e-03 | 7.92e-03 | 4.90e-03 | 35 |
| hsa0435021 | Prostate | Tumor | TGF-beta signaling pathway | 39/1791 | 108/8465 | 2.33e-04 | 1.35e-03 | 8.39e-04 | 39 |
| hsa0435031 | Prostate | Tumor | TGF-beta signaling pathway | 39/1791 | 108/8465 | 2.33e-04 | 1.35e-03 | 8.39e-04 | 39 |
| Page: 1 |
Top |
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 |
Top |
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 |
| ID4 | SURF | Endometrium | Healthy | GRN,LINC01541,MAOA, etc. | 4.53e-01 |  |
| ID4 | GDT | Oral cavity | ADJ | C11orf96,COL18A1,COL4A1, etc. | 1.45e-01 |  |
| ID4 | cDC | Oral cavity | LP | C11orf96,COL18A1,COL4A1, etc. | 1.20e-01 |  |
| ID4 | cDC | Oral cavity | OSCC | C11orf96,COL18A1,COL4A1, etc. | 5.64e-01 |  |
| ID4 | BN | Thyroid | ADJ | TFF3,TG,TPO, etc. | 1.09e-02 |  |
| ID4 | pDC | Thyroid | ADJ | TFF3,TG,TPO, etc. | 1.68e-02 | |
| ID4 | pDC | Thyroid | ATC | TFF3,TG,TPO, etc. | 5.72e-03 |  |
| ID4 | BMEM | Thyroid | ATC | TFF3,TG,TPO, etc. | 0.00e+00 | |
| ID4 | PLA | Thyroid | ATC | TFF3,TG,TPO, etc. | 1.69e-02 | |
| ID4 | GC | Thyroid | ATC | TFF3,TG,TPO, etc. | 0.00e+00 | |
| ∗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 2 3 |
Top |
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 |
| ID4 | SNV | Missense_Mutation | c.320N>T | p.Ala107Val | p.A107V | P47928 | protein_coding | tolerated(0.16) | benign(0.236) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ID4 | SNV | Missense_Mutation | novel | c.276G>T | p.Glu92Asp | p.E92D | P47928 | protein_coding | deleterious(0) | benign(0.239) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| ID4 | SNV | Missense_Mutation | novel | c.374N>G | p.His125Arg | p.H125R | P47928 | protein_coding | tolerated(0.85) | benign(0) | TCGA-90-7964-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| ID4 | SNV | Missense_Mutation | novel | c.182N>T | p.Ala61Val | p.A61V | P47928 | protein_coding | tolerated(1) | benign(0.005) | TCGA-BR-8591-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 |
Top |
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 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |