|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RFTN1 |
Gene summary for RFTN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RFTN1 | Gene ID | 23180 |
| Gene name | raftlin, lipid raft linker 1 | |
| Gene Alias | MIG2 | |
| Cytomap | 3p24.3 | |
| Gene Type | protein-coding | GO ID | GO:0001765 | UniProtAcc | Q14699 |
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 |
| 23180 | RFTN1 | HCC1_Meng | Human | Liver | HCC | 5.82e-09 | -2.59e-02 | 0.0246 |
| 23180 | RFTN1 | HCC1 | Human | Liver | HCC | 9.29e-07 | 3.97e+00 | 0.5336 |
| 23180 | RFTN1 | HCC2 | Human | Liver | HCC | 1.65e-17 | 4.58e+00 | 0.5341 |
| 23180 | RFTN1 | Pt13.b | Human | Liver | HCC | 2.70e-02 | 1.27e-01 | 0.0251 |
| 23180 | RFTN1 | S027 | Human | Liver | HCC | 7.12e-04 | 4.45e-01 | 0.2446 |
| 23180 | RFTN1 | S028 | Human | Liver | HCC | 2.32e-09 | 6.79e-01 | 0.2503 |
| 23180 | RFTN1 | S029 | Human | Liver | HCC | 6.00e-07 | 4.18e-01 | 0.2581 |
| 23180 | RFTN1 | EOLP-1 | Human | Oral cavity | EOLP | 2.23e-35 | 8.70e-01 | -0.0202 |
| 23180 | RFTN1 | EOLP-2 | Human | Oral cavity | EOLP | 3.27e-09 | 4.87e-01 | -0.0203 |
| 23180 | RFTN1 | NEOLP-1 | Human | Oral cavity | NEOLP | 8.71e-17 | 5.46e-01 | -0.0194 |
| 23180 | RFTN1 | NEOLP-2 | Human | Oral cavity | NEOLP | 2.57e-03 | 3.23e-01 | -0.0196 |
| 23180 | RFTN1 | NEOLP-3 | Human | Oral cavity | NEOLP | 1.87e-12 | 4.69e-01 | -0.0191 |
| 23180 | RFTN1 | male-WTA | Human | Thyroid | PTC | 1.51e-18 | 1.69e-01 | 0.1037 |
| 23180 | RFTN1 | PTC01 | Human | Thyroid | PTC | 5.99e-08 | 1.30e-01 | 0.1899 |
| 23180 | RFTN1 | PTC04 | Human | Thyroid | PTC | 1.68e-10 | 1.19e-01 | 0.1927 |
| 23180 | RFTN1 | PTC05 | Human | Thyroid | PTC | 8.85e-10 | 4.63e-01 | 0.2065 |
| 23180 | RFTN1 | PTC06 | Human | Thyroid | PTC | 4.94e-22 | 5.18e-01 | 0.2057 |
| 23180 | RFTN1 | PTC07 | Human | Thyroid | PTC | 7.02e-23 | 3.65e-01 | 0.2044 |
| 23180 | RFTN1 | ATC11 | Human | Thyroid | ATC | 1.63e-06 | 3.83e-01 | 0.3386 |
| 23180 | RFTN1 | ATC12 | Human | Thyroid | ATC | 1.24e-03 | 1.10e-01 | 0.34 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:000640321 | Liver | HCC | RNA localization | 151/7958 | 201/18723 | 3.72e-21 | 5.89e-19 | 151 |
| GO:005123621 | Liver | HCC | establishment of RNA localization | 121/7958 | 166/18723 | 1.61e-15 | 1.19e-13 | 121 |
| GO:005065711 | Liver | HCC | nucleic acid transport | 118/7958 | 163/18723 | 8.30e-15 | 5.60e-13 | 118 |
| GO:005065811 | Liver | HCC | RNA transport | 118/7958 | 163/18723 | 8.30e-15 | 5.60e-13 | 118 |
| GO:001593111 | Liver | HCC | nucleobase-containing compound transport | 150/7958 | 222/18723 | 3.17e-14 | 2.03e-12 | 150 |
| GO:009015012 | Liver | HCC | establishment of protein localization to membrane | 168/7958 | 260/18723 | 4.07e-13 | 2.13e-11 | 168 |
| GO:00022211 | Liver | HCC | pattern recognition receptor signaling pathway | 107/7958 | 172/18723 | 1.37e-07 | 2.58e-06 | 107 |
| GO:001988212 | Liver | HCC | antigen processing and presentation | 65/7958 | 106/18723 | 7.06e-05 | 6.37e-04 | 65 |
| GO:004409111 | Liver | HCC | membrane biogenesis | 37/7958 | 55/18723 | 1.79e-04 | 1.41e-03 | 37 |
| GO:007170911 | Liver | HCC | membrane assembly | 34/7958 | 50/18723 | 2.38e-04 | 1.79e-03 | 34 |
| GO:0002224 | Liver | HCC | toll-like receptor signaling pathway | 67/7958 | 121/18723 | 2.87e-03 | 1.34e-02 | 67 |
| GO:00315791 | Liver | HCC | membrane raft organization | 17/7958 | 25/18723 | 8.94e-03 | 3.45e-02 | 17 |
| GO:00017651 | Liver | HCC | membrane raft assembly | 9/7958 | 11/18723 | 9.51e-03 | 3.60e-02 | 9 |
| GO:004592711 | Liver | HCC | positive regulation of growth | 128/7958 | 259/18723 | 1.41e-02 | 4.99e-02 | 128 |
| GO:000276413 | Oral cavity | EOLP | immune response-regulating signaling pathway | 108/2218 | 468/18723 | 4.04e-12 | 7.34e-10 | 108 |
| GO:000640323 | Oral cavity | EOLP | RNA localization | 57/2218 | 201/18723 | 1.62e-10 | 1.68e-08 | 57 |
| GO:001988224 | Oral cavity | EOLP | antigen processing and presentation | 36/2218 | 106/18723 | 1.96e-09 | 1.26e-07 | 36 |
| GO:001593121 | Oral cavity | EOLP | nucleobase-containing compound transport | 58/2218 | 222/18723 | 3.44e-09 | 2.10e-07 | 58 |
| GO:005065721 | Oral cavity | EOLP | nucleic acid transport | 47/2218 | 163/18723 | 3.53e-09 | 2.12e-07 | 47 |
| GO:005065821 | Oral cavity | EOLP | RNA transport | 47/2218 | 163/18723 | 3.53e-09 | 2.12e-07 | 47 |
| Page: 1 2 3 4 5 |
| 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 |
| RFTN1 | SNV | Missense_Mutation | c.379G>C | p.Asp127His | p.D127H | Q14699 | protein_coding | deleterious(0) | possibly_damaging(0.824) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RFTN1 | SNV | Missense_Mutation | c.749N>T | p.Ser250Leu | p.S250L | Q14699 | protein_coding | tolerated(0.26) | benign(0.003) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RFTN1 | insertion | Nonsense_Mutation | novel | c.284_285insAGAATGATGT | p.Pro96GlufsTer2 | p.P96Efs*2 | Q14699 | protein_coding | TCGA-A8-A08S-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| RFTN1 | insertion | Frame_Shift_Ins | novel | c.283_284insAGCATATGCC | p.Thr95LysfsTer11 | p.T95Kfs*11 | Q14699 | protein_coding | TCGA-A8-A08S-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| RFTN1 | SNV | Missense_Mutation | rs758444396 | c.650G>A | p.Arg217Lys | p.R217K | Q14699 | protein_coding | tolerated(0.91) | benign(0) | TCGA-EK-A2RK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| RFTN1 | SNV | Missense_Mutation | rs368097786 | c.530N>T | p.Pro177Leu | p.P177L | Q14699 | protein_coding | tolerated(0.82) | benign(0) | TCGA-5M-AAT4-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
| RFTN1 | SNV | Missense_Mutation | novel | c.1073N>G | p.Ala358Gly | p.A358G | Q14699 | protein_coding | tolerated(0.47) | possibly_damaging(0.552) | TCGA-A6-3807-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Ancillary | leucovorin | SD |
| RFTN1 | SNV | Missense_Mutation | novel | c.1072N>T | p.Ala358Ser | p.A358S | Q14699 | protein_coding | tolerated(0.77) | possibly_damaging(0.579) | TCGA-A6-3807-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Ancillary | leucovorin | SD |
| RFTN1 | SNV | Missense_Mutation | rs781778331 | c.241N>A | p.Ala81Thr | p.A81T | Q14699 | protein_coding | tolerated(0.16) | benign(0.207) | TCGA-AA-3660-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RFTN1 | SNV | Missense_Mutation | novel | c.143N>T | p.Ala48Val | p.A48V | Q14699 | protein_coding | tolerated(0.28) | possibly_damaging(0.544) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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 |