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Gene: GCFC2 |
Gene summary for GCFC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GCFC2 | Gene ID | 6936 |
| Gene name | GC-rich sequence DNA-binding factor 2 | |
| Gene Alias | C2orf3 | |
| Cytomap | 2p12 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | A4UHR0 |
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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 |
| 6936 | GCFC2 | LZE4T | Human | Esophagus | ESCC | 7.63e-07 | 1.56e-01 | 0.0811 |
| 6936 | GCFC2 | LZE7T | Human | Esophagus | ESCC | 2.48e-06 | 1.71e-01 | 0.0667 |
| 6936 | GCFC2 | LZE24T | Human | Esophagus | ESCC | 6.12e-19 | 2.40e-01 | 0.0596 |
| 6936 | GCFC2 | LZE21T | Human | Esophagus | ESCC | 1.76e-02 | 1.34e-01 | 0.0655 |
| 6936 | GCFC2 | P1T-E | Human | Esophagus | ESCC | 4.74e-02 | 8.84e-02 | 0.0875 |
| 6936 | GCFC2 | P2T-E | Human | Esophagus | ESCC | 5.63e-28 | 5.74e-01 | 0.1177 |
| 6936 | GCFC2 | P4T-E | Human | Esophagus | ESCC | 4.92e-20 | 4.89e-01 | 0.1323 |
| 6936 | GCFC2 | P5T-E | Human | Esophagus | ESCC | 8.41e-14 | 1.26e-01 | 0.1327 |
| 6936 | GCFC2 | P8T-E | Human | Esophagus | ESCC | 1.41e-20 | 1.22e-01 | 0.0889 |
| 6936 | GCFC2 | P9T-E | Human | Esophagus | ESCC | 4.10e-07 | 7.97e-02 | 0.1131 |
| 6936 | GCFC2 | P10T-E | Human | Esophagus | ESCC | 8.25e-25 | 3.26e-01 | 0.116 |
| 6936 | GCFC2 | P11T-E | Human | Esophagus | ESCC | 1.19e-10 | 3.45e-01 | 0.1426 |
| 6936 | GCFC2 | P12T-E | Human | Esophagus | ESCC | 2.99e-26 | 4.44e-01 | 0.1122 |
| 6936 | GCFC2 | P15T-E | Human | Esophagus | ESCC | 3.84e-14 | 3.14e-01 | 0.1149 |
| 6936 | GCFC2 | P16T-E | Human | Esophagus | ESCC | 1.91e-25 | 4.59e-01 | 0.1153 |
| 6936 | GCFC2 | P20T-E | Human | Esophagus | ESCC | 1.33e-14 | 3.87e-01 | 0.1124 |
| 6936 | GCFC2 | P21T-E | Human | Esophagus | ESCC | 4.46e-21 | 3.21e-01 | 0.1617 |
| 6936 | GCFC2 | P22T-E | Human | Esophagus | ESCC | 1.00e-13 | 1.61e-01 | 0.1236 |
| 6936 | GCFC2 | P23T-E | Human | Esophagus | ESCC | 7.41e-19 | 4.58e-01 | 0.108 |
| 6936 | GCFC2 | P24T-E | Human | Esophagus | ESCC | 5.23e-11 | 2.27e-01 | 0.1287 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
| GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
| GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
| GO:000024514 | Esophagus | ESCC | spliceosomal complex assembly | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
| GO:00226137 | Liver | NAFLD | ribonucleoprotein complex biogenesis | 76/1882 | 463/18723 | 1.19e-05 | 3.67e-04 | 76 |
| GO:00226187 | Liver | NAFLD | ribonucleoprotein complex assembly | 42/1882 | 220/18723 | 3.40e-05 | 8.80e-04 | 42 |
| GO:00083807 | Liver | NAFLD | RNA splicing | 70/1882 | 434/18723 | 4.62e-05 | 1.10e-03 | 70 |
| GO:00718267 | Liver | NAFLD | ribonucleoprotein complex subunit organization | 42/1882 | 227/18723 | 7.21e-05 | 1.51e-03 | 42 |
| GO:00003777 | Liver | NAFLD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1882 | 320/18723 | 6.21e-04 | 8.18e-03 | 51 |
| GO:00003987 | Liver | NAFLD | mRNA splicing, via spliceosome | 51/1882 | 320/18723 | 6.21e-04 | 8.18e-03 | 51 |
| GO:00003757 | Liver | NAFLD | RNA splicing, via transesterification reactions | 51/1882 | 324/18723 | 8.28e-04 | 1.02e-02 | 51 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:000838022 | Liver | HCC | RNA splicing | 313/7958 | 434/18723 | 1.36e-36 | 1.73e-33 | 313 |
| GO:000037522 | Liver | HCC | RNA splicing, via transesterification reactions | 228/7958 | 324/18723 | 1.47e-24 | 4.06e-22 | 228 |
| GO:000037722 | Liver | HCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 224/7958 | 320/18723 | 1.16e-23 | 2.62e-21 | 224 |
| GO:000039822 | Liver | HCC | mRNA splicing, via spliceosome | 224/7958 | 320/18723 | 1.16e-23 | 2.62e-21 | 224 |
| Page: 1 2 3 |
| 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 |
| GCFC2 | SNV | Missense_Mutation | c.550N>A | p.Asp184Asn | p.D184N | P16383 | protein_coding | deleterious(0.03) | benign(0.038) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| GCFC2 | SNV | Missense_Mutation | c.517N>C | p.Glu173Gln | p.E173Q | P16383 | protein_coding | tolerated(0.28) | benign(0.021) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GCFC2 | SNV | Missense_Mutation | novel | c.1757N>C | p.Arg586Thr | p.R586T | P16383 | protein_coding | tolerated(0.13) | benign(0.152) | TCGA-C8-A8HP-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| GCFC2 | SNV | Missense_Mutation | novel | c.2338G>A | p.Glu780Lys | p.E780K | P16383 | protein_coding | tolerated_low_confidence(0.39) | benign(0.001) | TCGA-C5-A7UI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| GCFC2 | SNV | Missense_Mutation | c.2287N>A | p.Glu763Lys | p.E763K | P16383 | protein_coding | tolerated(0.12) | benign(0.005) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GCFC2 | SNV | Missense_Mutation | rs373951174 | c.889G>A | p.Val297Ile | p.V297I | P16383 | protein_coding | tolerated(0.82) | benign(0) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GCFC2 | SNV | Missense_Mutation | rs767780666 | c.1964N>A | p.Arg655His | p.R655H | P16383 | protein_coding | tolerated(0.35) | benign(0.003) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| GCFC2 | SNV | Missense_Mutation | rs773928373 | c.2038N>T | p.Arg680Cys | p.R680C | P16383 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GCFC2 | SNV | Missense_Mutation | novel | c.2188N>G | p.Leu730Val | p.L730V | P16383 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GCFC2 | insertion | Frame_Shift_Ins | novel | c.2127dupA | p.Trp710MetfsTer3 | p.W710Mfs*3 | P16383 | protein_coding | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| Page: 1 |
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