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Gene: FERMT1 |
Gene summary for FERMT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FERMT1 | Gene ID | 55612 |
| Gene name | FERM domain containing kindlin 1 | |
| Gene Alias | C20orf42 | |
| Cytomap | 20p12.3 | |
| Gene Type | protein-coding | GO ID | GO:0001667 | UniProtAcc | Q49AC8 |
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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 |
| 55612 | FERMT1 | CA_HPV_1 | Human | Cervix | CC | 5.04e-03 | -1.92e-01 | 0.0264 |
| 55612 | FERMT1 | CA_HPV_3 | Human | Cervix | CC | 1.01e-09 | 2.31e-01 | 0.0414 |
| 55612 | FERMT1 | CCI_3 | Human | Cervix | CC | 4.32e-02 | 4.23e-01 | 0.516 |
| 55612 | FERMT1 | Tumor | Human | Cervix | CC | 1.52e-11 | 3.64e-01 | 0.1241 |
| 55612 | FERMT1 | sample3 | Human | Cervix | CC | 2.91e-24 | 5.17e-01 | 0.1387 |
| 55612 | FERMT1 | T3 | Human | Cervix | CC | 1.55e-20 | 5.01e-01 | 0.1389 |
| 55612 | FERMT1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.33e-12 | 9.55e-01 | -0.0811 |
| 55612 | FERMT1 | HTA11_78_2000001011 | Human | Colorectum | AD | 9.53e-03 | 4.89e-01 | -0.1088 |
| 55612 | FERMT1 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.58e-06 | 5.02e-01 | -0.1954 |
| 55612 | FERMT1 | HTA11_411_2000001011 | Human | Colorectum | SER | 4.03e-02 | 7.19e-01 | -0.2602 |
| 55612 | FERMT1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.11e-11 | 1.03e+00 | -0.059 |
| 55612 | FERMT1 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.29e-31 | 1.39e+00 | 0.096 |
| 55612 | FERMT1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 1.02e-08 | 9.33e-01 | 0.0131 |
| 55612 | FERMT1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.45e-06 | 7.31e-01 | 0.0338 |
| 55612 | FERMT1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.08e-15 | 8.15e-01 | 0.0674 |
| 55612 | FERMT1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.34e-25 | 1.38e+00 | 0.0588 |
| 55612 | FERMT1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.22e-10 | 6.88e-01 | 0.294 |
| 55612 | FERMT1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 5.30e-07 | 6.89e-01 | 0.281 |
| 55612 | FERMT1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 9.70e-06 | 6.70e-01 | 0.3859 |
| 55612 | FERMT1 | A002-C-010 | Human | Colorectum | FAP | 8.13e-04 | 2.75e-01 | 0.242 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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 | ||
| 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 |
| ∗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:00066067 | Cervix | CC | protein import into nucleus | 37/2311 | 155/18723 | 5.13e-05 | 7.71e-04 | 37 |
| GO:19030368 | Cervix | CC | positive regulation of response to wounding | 21/2311 | 72/18723 | 1.10e-04 | 1.39e-03 | 21 |
| GO:00903037 | Cervix | CC | positive regulation of wound healing | 18/2311 | 59/18723 | 1.78e-04 | 2.09e-03 | 18 |
| GO:00071786 | Cervix | CC | transmembrane receptor protein serine/threonine kinase signaling pathway | 67/2311 | 355/18723 | 2.39e-04 | 2.67e-03 | 67 |
| GO:00716344 | Cervix | CC | regulation of transforming growth factor beta production | 14/2311 | 41/18723 | 2.49e-04 | 2.77e-03 | 14 |
| GO:00436164 | Cervix | CC | keratinocyte proliferation | 15/2311 | 46/18723 | 2.70e-04 | 2.97e-03 | 15 |
| GO:00716043 | Cervix | CC | transforming growth factor beta production | 14/2311 | 43/18723 | 4.37e-04 | 4.38e-03 | 14 |
| GO:19001808 | Cervix | CC | regulation of protein localization to nucleus | 31/2311 | 136/18723 | 4.76e-04 | 4.69e-03 | 31 |
| GO:00715595 | Cervix | CC | response to transforming growth factor beta | 50/2311 | 256/18723 | 6.31e-04 | 5.91e-03 | 50 |
| GO:00715605 | Cervix | CC | cellular response to transforming growth factor beta stimulus | 49/2311 | 250/18723 | 6.55e-04 | 6.05e-03 | 49 |
| GO:00901627 | Cervix | CC | establishment of epithelial cell polarity | 11/2311 | 31/18723 | 7.87e-04 | 6.96e-03 | 11 |
| GO:00336272 | Cervix | CC | cell adhesion mediated by integrin | 19/2311 | 72/18723 | 9.11e-04 | 7.81e-03 | 19 |
| GO:0035313 | Cervix | CC | wound healing, spreading of epidermal cells | 8/2311 | 19/18723 | 1.14e-03 | 9.34e-03 | 8 |
| GO:00301784 | Cervix | CC | negative regulation of Wnt signaling pathway | 35/2311 | 170/18723 | 1.52e-03 | 1.17e-02 | 35 |
| GO:00900901 | Cervix | CC | negative regulation of canonical Wnt signaling pathway | 29/2311 | 137/18723 | 2.40e-03 | 1.70e-02 | 29 |
| GO:19045896 | Cervix | CC | regulation of protein import | 16/2311 | 63/18723 | 3.42e-03 | 2.22e-02 | 16 |
| GO:00071795 | Cervix | CC | transforming growth factor beta receptor signaling pathway | 38/2311 | 198/18723 | 3.62e-03 | 2.31e-02 | 38 |
| GO:00019548 | Cervix | CC | positive regulation of cell-matrix adhesion | 15/2311 | 58/18723 | 3.75e-03 | 2.38e-02 | 15 |
| GO:0030198 | Cervix | CC | extracellular matrix organization | 52/2311 | 301/18723 | 7.43e-03 | 3.98e-02 | 52 |
| GO:0043062 | Cervix | CC | extracellular structure organization | 52/2311 | 302/18723 | 7.92e-03 | 4.17e-02 | 52 |
| 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 35 36 37 38 39 40 41 42 43 44 45 46 47 |
| 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 |
| FERMT1 | SNV | Missense_Mutation | c.1870N>A | p.Glu624Lys | p.E624K | Q9BQL6 | protein_coding | deleterious(0.01) | possibly_damaging(0.833) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| FERMT1 | SNV | Missense_Mutation | c.447G>C | p.Lys149Asn | p.K149N | Q9BQL6 | protein_coding | tolerated(0.22) | probably_damaging(0.983) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FERMT1 | SNV | Missense_Mutation | c.70G>C | p.Glu24Gln | p.E24Q | Q9BQL6 | protein_coding | tolerated(0.18) | benign(0.101) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FERMT1 | SNV | Missense_Mutation | c.509N>A | p.Ser170Tyr | p.S170Y | Q9BQL6 | protein_coding | tolerated(0.23) | possibly_damaging(0.703) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FERMT1 | SNV | Missense_Mutation | c.2028N>T | p.Gln676His | p.Q676H | Q9BQL6 | protein_coding | tolerated(0.94) | possibly_damaging(0.732) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FERMT1 | SNV | Missense_Mutation | c.1024G>A | p.Glu342Lys | p.E342K | Q9BQL6 | protein_coding | deleterious(0.01) | benign(0.232) | TCGA-AO-A0JC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD | |
| FERMT1 | SNV | Missense_Mutation | novel | c.757T>C | p.Ser253Pro | p.S253P | Q9BQL6 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
| FERMT1 | SNV | Missense_Mutation | rs143876620 | c.1603N>T | p.Arg535Trp | p.R535W | Q9BQL6 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| FERMT1 | SNV | Missense_Mutation | novel | c.790N>A | p.Glu264Lys | p.E264K | Q9BQL6 | protein_coding | deleterious(0.02) | probably_damaging(0.976) | TCGA-MY-A5BF-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | CR |
| FERMT1 | SNV | Missense_Mutation | c.1258N>A | p.Leu420Ile | p.L420I | Q9BQL6 | protein_coding | deleterious(0.03) | benign(0.236) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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