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Gene: IGFBP4 |
Gene summary for IGFBP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | IGFBP4 | Gene ID | 3487 |
| Gene name | insulin like growth factor binding protein 4 | |
| Gene Alias | BP-4 | |
| Cytomap | 17q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A024R1U8 |
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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 |
| 3487 | IGFBP4 | EEC-subject4 | Human | Endometrium | EEC | 6.49e-56 | -1.03e+00 | -0.2571 |
| 3487 | IGFBP4 | EEC-subject5 | Human | Endometrium | EEC | 5.74e-35 | -8.22e-01 | -0.249 |
| 3487 | IGFBP4 | GSM5276934 | Human | Endometrium | EEC | 7.50e-27 | -6.65e-01 | -0.0913 |
| 3487 | IGFBP4 | GSM5276935 | Human | Endometrium | EEC | 7.06e-59 | -1.01e+00 | -0.123 |
| 3487 | IGFBP4 | GSM5276937 | Human | Endometrium | EEC | 4.09e-43 | -9.18e-01 | -0.0897 |
| 3487 | IGFBP4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 4.67e-77 | -1.39e+00 | -0.1869 |
| 3487 | IGFBP4 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 3.54e-66 | -1.34e+00 | -0.1875 |
| 3487 | IGFBP4 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 3.47e-72 | -1.33e+00 | -0.1883 |
| 3487 | IGFBP4 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 2.16e-24 | -5.84e-01 | -0.1934 |
| 3487 | IGFBP4 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 4.14e-99 | -1.38e+00 | -0.1917 |
| 3487 | IGFBP4 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 5.11e-97 | -1.38e+00 | -0.1916 |
| 3487 | IGFBP4 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 4.50e-42 | -8.88e-01 | -0.1269 |
| 3487 | IGFBP4 | LZE4T | Human | Esophagus | ESCC | 5.12e-05 | -1.16e-01 | 0.0811 |
| 3487 | IGFBP4 | LZE20T | Human | Esophagus | ESCC | 1.35e-07 | 8.98e-01 | 0.0662 |
| 3487 | IGFBP4 | LZE22T | Human | Esophagus | ESCC | 1.84e-08 | 1.52e+00 | 0.068 |
| 3487 | IGFBP4 | LZE24T | Human | Esophagus | ESCC | 2.46e-11 | 4.52e-01 | 0.0596 |
| 3487 | IGFBP4 | LZE21T | Human | Esophagus | ESCC | 1.49e-02 | 6.30e-01 | 0.0655 |
| 3487 | IGFBP4 | P1T-E | Human | Esophagus | ESCC | 1.68e-13 | 1.44e+00 | 0.0875 |
| 3487 | IGFBP4 | P2T-E | Human | Esophagus | ESCC | 1.33e-128 | 3.61e+00 | 0.1177 |
| 3487 | IGFBP4 | P4T-E | Human | Esophagus | ESCC | 5.60e-71 | 2.43e+00 | 0.1323 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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. |
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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). |
| 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:0016049 | Colorectum | AD | cell growth | 143/3918 | 482/18723 | 2.83e-06 | 8.09e-05 | 143 |
| GO:0001558 | Colorectum | AD | regulation of cell growth | 124/3918 | 414/18723 | 7.67e-06 | 1.86e-04 | 124 |
| GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
| GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
| GO:0019318 | Colorectum | AD | hexose metabolic process | 77/3918 | 237/18723 | 1.96e-05 | 4.01e-04 | 77 |
| GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
| GO:0044262 | Colorectum | AD | cellular carbohydrate metabolic process | 87/3918 | 283/18723 | 6.00e-05 | 1.01e-03 | 87 |
| GO:0005996 | Colorectum | AD | monosaccharide metabolic process | 80/3918 | 257/18723 | 7.31e-05 | 1.17e-03 | 80 |
| GO:0060070 | Colorectum | AD | canonical Wnt signaling pathway | 90/3918 | 303/18723 | 1.76e-04 | 2.38e-03 | 90 |
| GO:0060828 | Colorectum | AD | regulation of canonical Wnt signaling pathway | 77/3918 | 253/18723 | 2.19e-04 | 2.87e-03 | 77 |
| GO:0006006 | Colorectum | AD | glucose metabolic process | 62/3918 | 196/18723 | 2.76e-04 | 3.39e-03 | 62 |
| GO:0050673 | Colorectum | AD | epithelial cell proliferation | 119/3918 | 437/18723 | 8.75e-04 | 8.51e-03 | 119 |
| GO:0006109 | Colorectum | AD | regulation of carbohydrate metabolic process | 55/3918 | 178/18723 | 1.10e-03 | 1.01e-02 | 55 |
| GO:0062012 | Colorectum | AD | regulation of small molecule metabolic process | 93/3918 | 334/18723 | 1.46e-03 | 1.24e-02 | 93 |
| GO:00160551 | Colorectum | SER | Wnt signaling pathway | 97/2897 | 444/18723 | 2.02e-04 | 3.68e-03 | 97 |
| GO:01987381 | Colorectum | SER | cell-cell signaling by wnt | 97/2897 | 446/18723 | 2.39e-04 | 4.11e-03 | 97 |
| GO:00301111 | Colorectum | SER | regulation of Wnt signaling pathway | 75/2897 | 328/18723 | 2.47e-04 | 4.20e-03 | 75 |
| GO:00015581 | Colorectum | SER | regulation of cell growth | 90/2897 | 414/18723 | 4.00e-04 | 6.02e-03 | 90 |
| GO:00193181 | Colorectum | SER | hexose metabolic process | 56/2897 | 237/18723 | 6.19e-04 | 8.42e-03 | 56 |
| GO:0048009 | Colorectum | SER | insulin-like growth factor receptor signaling pathway | 14/2897 | 37/18723 | 7.80e-04 | 9.87e-03 | 14 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| IGFBP4 | SNV | Missense_Mutation | c.529N>A | p.Glu177Lys | p.E177K | P22692 | protein_coding | deleterious(0.01) | probably_damaging(0.978) | TCGA-D8-A27W-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| IGFBP4 | insertion | Nonsense_Mutation | novel | c.382_383insAAGCCGAAGAA | p.Phe128Ter | p.F128* | P22692 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| IGFBP4 | insertion | In_Frame_Ins | novel | c.383_384insCCC | p.Phe128_Ser129insPro | p.F128_S129insP | P22692 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| IGFBP4 | SNV | Missense_Mutation | rs745961147 | c.482C>T | p.Ala161Val | p.A161V | P22692 | protein_coding | tolerated(0.52) | benign(0) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| IGFBP4 | SNV | Missense_Mutation | c.617G>A | p.Arg206His | p.R206H | P22692 | protein_coding | tolerated(0.1) | probably_damaging(0.963) | TCGA-AA-3833-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| IGFBP4 | SNV | Missense_Mutation | novel | c.740T>G | p.Leu247Arg | p.L247R | P22692 | protein_coding | tolerated(0.05) | probably_damaging(0.992) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| IGFBP4 | SNV | Missense_Mutation | c.673A>G | p.Lys225Glu | p.K225E | P22692 | protein_coding | tolerated(0.1) | probably_damaging(0.998) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| IGFBP4 | deletion | Frame_Shift_Del | rs778799414 | c.123delC | p.Val42TrpfsTer52 | p.V42Wfs*52 | P22692 | protein_coding | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| IGFBP4 | deletion | Frame_Shift_Del | rs778799414 | c.117delN | p.Val42TrpfsTer52 | p.V42Wfs*52 | P22692 | protein_coding | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| IGFBP4 | SNV | Missense_Mutation | rs755831062 | c.430N>A | p.Ala144Thr | p.A144T | P22692 | protein_coding | tolerated(0.18) | benign(0.129) | TCGA-A5-A1OF-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 |
| 3487 | IGFBP4 | DRUGGABLE GENOME | PMSG | 9258879 |
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