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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004206010 | Cervix | CC | wound healing | 109/2311 | 422/18723 | 1.84e-14 | 1.57e-11 | 109 |
GO:001081010 | Cervix | CC | regulation of cell-substrate adhesion | 69/2311 | 221/18723 | 8.57e-14 | 5.69e-11 | 69 |
GO:00315898 | Cervix | CC | cell-substrate adhesion | 96/2311 | 363/18723 | 1.48e-13 | 8.85e-11 | 96 |
GO:009013210 | Cervix | CC | epithelium migration | 90/2311 | 360/18723 | 2.45e-11 | 6.11e-09 | 90 |
GO:00016679 | Cervix | CC | ameboidal-type cell migration | 110/2311 | 475/18723 | 2.66e-11 | 6.36e-09 | 110 |
GO:001063110 | Cervix | CC | epithelial cell migration | 89/2311 | 357/18723 | 3.72e-11 | 8.54e-09 | 89 |
GO:00085446 | Cervix | CC | epidermis development | 83/2311 | 324/18723 | 3.91e-11 | 8.54e-09 | 83 |
GO:00071639 | Cervix | CC | establishment or maintenance of cell polarity | 63/2311 | 218/18723 | 4.25e-11 | 8.76e-09 | 63 |
GO:009013010 | Cervix | CC | tissue migration | 90/2311 | 365/18723 | 5.42e-11 | 1.05e-08 | 90 |
GO:00435884 | Cervix | CC | skin development | 71/2311 | 263/18723 | 8.04e-11 | 1.46e-08 | 71 |
GO:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
GO:004578510 | Cervix | CC | positive regulation of cell adhesion | 101/2311 | 437/18723 | 1.96e-10 | 3.08e-08 | 101 |
GO:00506737 | Cervix | CC | epithelial cell proliferation | 98/2311 | 437/18723 | 2.01e-09 | 2.15e-07 | 98 |
GO:004325410 | Cervix | CC | regulation of protein-containing complex assembly | 96/2311 | 428/18723 | 2.91e-09 | 3.05e-07 | 96 |
GO:00160557 | Cervix | CC | Wnt signaling pathway | 98/2311 | 444/18723 | 4.82e-09 | 4.65e-07 | 98 |
GO:01987387 | Cervix | CC | cell-cell signaling by wnt | 98/2311 | 446/18723 | 6.16e-09 | 5.58e-07 | 98 |
GO:00019528 | Cervix | CC | regulation of cell-matrix adhesion | 40/2311 | 128/18723 | 1.32e-08 | 1.04e-06 | 40 |
GO:00071608 | Cervix | CC | cell-matrix adhesion | 60/2311 | 233/18723 | 1.58e-08 | 1.23e-06 | 60 |
GO:00301117 | Cervix | CC | regulation of Wnt signaling pathway | 76/2311 | 328/18723 | 3.05e-08 | 2.08e-06 | 76 |
GO:00069139 | Cervix | CC | nucleocytoplasmic transport | 71/2311 | 301/18723 | 4.04e-08 | 2.54e-06 | 71 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 | novel | c.1424N>G | p.Lys475Arg | p.K475R | Q9BQL6 | protein_coding | tolerated(0.46) | benign(0.179) | TCGA-UF-A7JK-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
FERMT1 | SNV | Missense_Mutation | rs777736000 | c.764G>A | p.Arg255His | p.R255H | Q9BQL6 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-BR-6566-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
FERMT1 | SNV | Missense_Mutation | novel | c.1943N>A | p.Gly648Asp | p.G648D | Q9BQL6 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CG-5726-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
FERMT1 | SNV | Missense_Mutation | c.1973N>G | p.Lys658Arg | p.K658R | Q9BQL6 | protein_coding | tolerated(0.25) | possibly_damaging(0.677) | TCGA-F1-A448-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR | |
FERMT1 | SNV | Missense_Mutation | c.242N>C | p.Gly81Ala | p.G81A | Q9BQL6 | protein_coding | deleterious(0.03) | probably_damaging(0.972) | TCGA-HU-8602-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
FERMT1 | SNV | Missense_Mutation | c.1790N>G | p.Thr597Ser | p.T597S | Q9BQL6 | protein_coding | tolerated(0.31) | benign(0.012) | TCGA-HU-A4HD-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
FERMT1 | insertion | In_Frame_Ins | novel | c.452_453insGAA | p.Lys152dup | p.K152dup | Q9BQL6 | protein_coding | TCGA-HU-8604-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | doxifluridine | SD | ||
FERMT1 | insertion | In_Frame_Ins | novel | c.1020_1021insTCAAAATCA | p.Val340_Asp341insSerLysSer | p.V340_D341insSKS | Q9BQL6 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | 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 |
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