|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: GIGYF2 |
Gene summary for GIGYF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GIGYF2 | Gene ID | 26058 |
| Gene name | GRB10 interacting GYF protein 2 | |
| Gene Alias | GYF2 | |
| Cytomap | 2q37.1 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | Q6Y7W6 |
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 |
| 26058 | GIGYF2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.77e-19 | -6.46e-01 | 0.0155 |
| 26058 | GIGYF2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.47e-06 | -5.41e-01 | -0.1808 |
| 26058 | GIGYF2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 4.14e-02 | -7.21e-01 | 0.0216 |
| 26058 | GIGYF2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.74e-05 | -5.16e-01 | -0.1207 |
| 26058 | GIGYF2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.40e-03 | -6.63e-01 | -0.2061 |
| 26058 | GIGYF2 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.07e-04 | -3.72e-01 | 0.096 |
| 26058 | GIGYF2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 7.91e-05 | -5.23e-01 | 0.0338 |
| 26058 | GIGYF2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 7.29e-08 | -4.84e-01 | 0.0588 |
| 26058 | GIGYF2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.87e-09 | -4.47e-01 | 0.294 |
| 26058 | GIGYF2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.64e-09 | -4.26e-01 | 0.3005 |
| 26058 | GIGYF2 | A002-C-010 | Human | Colorectum | FAP | 4.19e-02 | -1.85e-01 | 0.242 |
| 26058 | GIGYF2 | A001-C-207 | Human | Colorectum | FAP | 1.92e-04 | -2.56e-01 | 0.1278 |
| 26058 | GIGYF2 | A015-C-203 | Human | Colorectum | FAP | 1.17e-30 | -4.08e-01 | -0.1294 |
| 26058 | GIGYF2 | A015-C-204 | Human | Colorectum | FAP | 4.42e-06 | -2.54e-01 | -0.0228 |
| 26058 | GIGYF2 | A014-C-040 | Human | Colorectum | FAP | 2.03e-08 | -6.08e-01 | -0.1184 |
| 26058 | GIGYF2 | A002-C-201 | Human | Colorectum | FAP | 2.83e-13 | -2.75e-01 | 0.0324 |
| 26058 | GIGYF2 | A002-C-203 | Human | Colorectum | FAP | 1.10e-04 | -1.81e-01 | 0.2786 |
| 26058 | GIGYF2 | A001-C-119 | Human | Colorectum | FAP | 8.65e-07 | 3.82e-02 | -0.1557 |
| 26058 | GIGYF2 | A001-C-108 | Human | Colorectum | FAP | 1.05e-14 | -1.28e-01 | -0.0272 |
| 26058 | GIGYF2 | A002-C-205 | Human | Colorectum | FAP | 6.31e-25 | -2.57e-01 | -0.1236 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 | ||
| 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. |
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:00342497 | Skin | AK | negative regulation of cellular amide metabolic process | 47/1910 | 273/18723 | 2.39e-04 | 2.62e-03 | 47 |
| GO:003465520 | Skin | AK | nucleobase-containing compound catabolic process | 64/1910 | 407/18723 | 3.01e-04 | 3.12e-03 | 64 |
| GO:006101417 | Skin | AK | positive regulation of mRNA catabolic process | 20/1910 | 87/18723 | 3.90e-04 | 3.74e-03 | 20 |
| GO:005077917 | Skin | AK | RNA destabilization | 20/1910 | 88/18723 | 4.57e-04 | 4.27e-03 | 20 |
| GO:00315719 | Skin | AK | mitotic G1 DNA damage checkpoint | 10/1910 | 30/18723 | 5.26e-04 | 4.79e-03 | 10 |
| GO:19019916 | Skin | AK | negative regulation of mitotic cell cycle phase transition | 33/1910 | 179/18723 | 5.67e-04 | 5.06e-03 | 33 |
| GO:20001344 | Skin | AK | negative regulation of G1/S transition of mitotic cell cycle | 19/1910 | 84/18723 | 6.68e-04 | 5.74e-03 | 19 |
| GO:00448199 | Skin | AK | mitotic G1/S transition checkpoint | 10/1910 | 31/18723 | 7.07e-04 | 6.01e-03 | 10 |
| GO:19019884 | Skin | AK | negative regulation of cell cycle phase transition | 42/1910 | 249/18723 | 7.65e-04 | 6.39e-03 | 42 |
| GO:19028074 | Skin | AK | negative regulation of cell cycle G1/S phase transition | 19/1910 | 93/18723 | 2.39e-03 | 1.57e-02 | 19 |
| GO:00000776 | Skin | AK | DNA damage checkpoint | 22/1910 | 115/18723 | 2.74e-03 | 1.74e-02 | 22 |
| GO:004670019 | Skin | AK | heterocycle catabolic process | 64/1910 | 445/18723 | 3.01e-03 | 1.88e-02 | 64 |
| GO:00109485 | Skin | AK | negative regulation of cell cycle process | 45/1910 | 294/18723 | 3.73e-03 | 2.22e-02 | 45 |
| GO:004427020 | Skin | AK | cellular nitrogen compound catabolic process | 64/1910 | 451/18723 | 4.11e-03 | 2.41e-02 | 64 |
| GO:001943919 | Skin | AK | aromatic compound catabolic process | 65/1910 | 467/18723 | 5.99e-03 | 3.24e-02 | 65 |
| GO:00315706 | Skin | AK | DNA integrity checkpoint | 22/1910 | 123/18723 | 6.33e-03 | 3.38e-02 | 22 |
| GO:00000755 | Skin | AK | cell cycle checkpoint | 28/1910 | 169/18723 | 6.83e-03 | 3.60e-02 | 28 |
| GO:190136119 | Skin | AK | organic cyclic compound catabolic process | 67/1910 | 495/18723 | 9.91e-03 | 4.80e-02 | 67 |
| GO:190331126 | Skin | cSCC | regulation of mRNA metabolic process | 162/4864 | 288/18723 | 5.90e-28 | 2.46e-25 | 162 |
| GO:000641729 | Skin | cSCC | regulation of translation | 226/4864 | 468/18723 | 8.78e-26 | 2.62e-23 | 226 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| ∗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 |
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 |
| GIGYF2 | SNV | Missense_Mutation | novel | c.2206N>T | p.Asp736Tyr | p.D736Y | Q6Y7W6 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-A7-A4SF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| GIGYF2 | SNV | Missense_Mutation | c.1021N>A | p.Glu341Lys | p.E341K | Q6Y7W6 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| GIGYF2 | SNV | Missense_Mutation | rs372418931 | c.3059N>T | p.Thr1020Met | p.T1020M | Q6Y7W6 | protein_coding | tolerated(0.46) | benign(0.441) | TCGA-E2-A15C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| GIGYF2 | insertion | Nonsense_Mutation | novel | c.3493_3494insTCTCCTGGGCTGGAATGTAGCTAGGACT | p.His1165LeufsTer7 | p.H1165Lfs*7 | Q6Y7W6 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| GIGYF2 | deletion | Frame_Shift_Del | c.734delN | p.Ala245ValfsTer56 | p.A245Vfs*56 | Q6Y7W6 | protein_coding | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| GIGYF2 | SNV | Missense_Mutation | c.3323N>A | p.Gly1108Glu | p.G1108E | Q6Y7W6 | protein_coding | deleterious(0) | benign(0.015) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD | |
| GIGYF2 | SNV | Missense_Mutation | c.712N>A | p.Glu238Lys | p.E238K | Q6Y7W6 | protein_coding | tolerated(0.1) | possibly_damaging(0.776) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| GIGYF2 | SNV | Missense_Mutation | rs754519471 | c.2402N>A | p.Arg801Gln | p.R801Q | Q6Y7W6 | protein_coding | tolerated(0.26) | benign(0.297) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| GIGYF2 | SNV | Missense_Mutation | novel | c.937N>A | p.Glu313Lys | p.E313K | Q6Y7W6 | protein_coding | deleterious(0.01) | possibly_damaging(0.857) | TCGA-ZJ-AB0H-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| GIGYF2 | SNV | Missense_Mutation | c.2423N>A | p.Arg808Gln | p.R808Q | Q6Y7W6 | protein_coding | deleterious(0.01) | probably_damaging(0.953) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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 |