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Gene: FRMD4A |
Gene summary for FRMD4A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FRMD4A | Gene ID | 55691 |
| Gene name | FERM domain containing 4A | |
| Gene Alias | CCAFCA | |
| Cytomap | 10p13 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9NW91 |
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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 |
| 55691 | FRMD4A | AEH-subject5 | Human | Endometrium | AEH | 2.99e-06 | 3.74e-01 | -0.2953 |
| 55691 | FRMD4A | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 4.96e-02 | -3.14e-02 | -0.1875 |
| 55691 | FRMD4A | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 4.92e-02 | -7.47e-02 | -0.1883 |
| 55691 | FRMD4A | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 5.10e-06 | 2.54e-01 | -0.1934 |
| 55691 | FRMD4A | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 2.19e-04 | -3.53e-02 | -0.1917 |
| 55691 | FRMD4A | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 5.68e-03 | 1.63e-02 | -0.1916 |
| 55691 | FRMD4A | LZE7T | Human | Esophagus | ESCC | 2.71e-02 | 1.52e-01 | 0.0667 |
| 55691 | FRMD4A | LZE24T | Human | Esophagus | ESCC | 4.64e-06 | 1.39e-01 | 0.0596 |
| 55691 | FRMD4A | P2T-E | Human | Esophagus | ESCC | 1.16e-61 | 1.47e+00 | 0.1177 |
| 55691 | FRMD4A | P4T-E | Human | Esophagus | ESCC | 1.88e-04 | 2.30e-01 | 0.1323 |
| 55691 | FRMD4A | P5T-E | Human | Esophagus | ESCC | 1.05e-06 | 1.09e-01 | 0.1327 |
| 55691 | FRMD4A | P8T-E | Human | Esophagus | ESCC | 5.12e-15 | 1.33e-01 | 0.0889 |
| 55691 | FRMD4A | P9T-E | Human | Esophagus | ESCC | 1.23e-04 | 1.18e-01 | 0.1131 |
| 55691 | FRMD4A | P10T-E | Human | Esophagus | ESCC | 8.94e-09 | 1.10e-01 | 0.116 |
| 55691 | FRMD4A | P11T-E | Human | Esophagus | ESCC | 5.67e-12 | 6.05e-01 | 0.1426 |
| 55691 | FRMD4A | P12T-E | Human | Esophagus | ESCC | 1.15e-11 | 3.18e-01 | 0.1122 |
| 55691 | FRMD4A | P15T-E | Human | Esophagus | ESCC | 2.70e-04 | 8.63e-02 | 0.1149 |
| 55691 | FRMD4A | P16T-E | Human | Esophagus | ESCC | 7.02e-52 | 8.84e-01 | 0.1153 |
| 55691 | FRMD4A | P19T-E | Human | Esophagus | ESCC | 1.34e-04 | 8.10e-01 | 0.1662 |
| 55691 | FRMD4A | P20T-E | Human | Esophagus | ESCC | 3.82e-09 | 1.22e-01 | 0.1124 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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. |
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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:190495115 | Endometrium | AEH | positive regulation of establishment of protein localization | 74/2100 | 319/18723 | 7.05e-10 | 6.51e-08 | 74 |
| GO:000716310 | Endometrium | AEH | establishment or maintenance of cell polarity | 54/2100 | 218/18723 | 1.30e-08 | 8.47e-07 | 54 |
| GO:005122215 | Endometrium | AEH | positive regulation of protein transport | 66/2100 | 303/18723 | 7.79e-08 | 3.99e-06 | 66 |
| GO:00300109 | Endometrium | AEH | establishment of cell polarity | 36/2100 | 143/18723 | 2.19e-06 | 6.49e-05 | 36 |
| GO:00510515 | Endometrium | AEH | negative regulation of transport | 79/2100 | 470/18723 | 1.51e-04 | 1.99e-03 | 79 |
| GO:00507087 | Endometrium | AEH | regulation of protein secretion | 49/2100 | 268/18723 | 3.83e-04 | 4.12e-03 | 49 |
| GO:00507149 | Endometrium | AEH | positive regulation of protein secretion | 28/2100 | 137/18723 | 1.17e-03 | 1.01e-02 | 28 |
| GO:00901628 | Endometrium | AEH | establishment of epithelial cell polarity | 10/2100 | 31/18723 | 1.48e-03 | 1.23e-02 | 10 |
| GO:00716927 | Endometrium | AEH | protein localization to extracellular region | 58/2100 | 368/18723 | 4.72e-03 | 3.00e-02 | 58 |
| GO:00093068 | Endometrium | AEH | protein secretion | 56/2100 | 359/18723 | 6.71e-03 | 3.94e-02 | 56 |
| GO:00355928 | Endometrium | AEH | establishment of protein localization to extracellular region | 56/2100 | 360/18723 | 7.10e-03 | 4.09e-02 | 56 |
| GO:190495116 | Endometrium | EEC | positive regulation of establishment of protein localization | 74/2168 | 319/18723 | 2.90e-09 | 2.10e-07 | 74 |
| GO:000716315 | Endometrium | EEC | establishment or maintenance of cell polarity | 56/2168 | 218/18723 | 5.41e-09 | 3.57e-07 | 56 |
| GO:005122216 | Endometrium | EEC | positive regulation of protein transport | 66/2168 | 303/18723 | 2.55e-07 | 1.09e-05 | 66 |
| GO:003001014 | Endometrium | EEC | establishment of cell polarity | 36/2168 | 143/18723 | 4.57e-06 | 1.15e-04 | 36 |
| GO:005105111 | Endometrium | EEC | negative regulation of transport | 80/2168 | 470/18723 | 2.53e-04 | 2.93e-03 | 80 |
| GO:005070813 | Endometrium | EEC | regulation of protein secretion | 50/2168 | 268/18723 | 4.33e-04 | 4.51e-03 | 50 |
| GO:009016213 | Endometrium | EEC | establishment of epithelial cell polarity | 10/2168 | 31/18723 | 1.89e-03 | 1.45e-02 | 10 |
| GO:005071412 | Endometrium | EEC | positive regulation of protein secretion | 28/2168 | 137/18723 | 1.89e-03 | 1.45e-02 | 28 |
| GO:007169213 | Endometrium | EEC | protein localization to extracellular region | 59/2168 | 368/18723 | 5.98e-03 | 3.56e-02 | 59 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| FRMD4A | SNV | Missense_Mutation | c.188N>C | p.Ile63Thr | p.I63T | Q9P2Q2 | protein_coding | tolerated(0.05) | probably_damaging(0.966) | TCGA-A1-A0SG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||
| FRMD4A | SNV | Missense_Mutation | novel | c.829N>A | p.Pro277Thr | p.P277T | Q9P2Q2 | protein_coding | tolerated(0.07) | benign(0.046) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| FRMD4A | SNV | Missense_Mutation | novel | c.1404G>T | p.Glu468Asp | p.E468D | Q9P2Q2 | protein_coding | tolerated(0.32) | possibly_damaging(0.489) | TCGA-AO-A0J3-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD |
| FRMD4A | SNV | Missense_Mutation | c.397N>T | p.Val133Phe | p.V133F | Q9P2Q2 | protein_coding | deleterious(0.05) | possibly_damaging(0.896) | TCGA-BH-A0C0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
| FRMD4A | SNV | Missense_Mutation | c.232N>T | p.Asp78Tyr | p.D78Y | Q9P2Q2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| FRMD4A | insertion | Frame_Shift_Ins | novel | c.1614_1615insTCTTGGGAAATTCTTAAAAAAACAGAACTGATCCCTCCCCCAACCCC | p.Ala539SerfsTer94 | p.A539Sfs*94 | Q9P2Q2 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| FRMD4A | SNV | Missense_Mutation | novel | c.2768C>T | p.Ala923Val | p.A923V | Q9P2Q2 | protein_coding | tolerated(0.19) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| FRMD4A | SNV | Missense_Mutation | c.1553G>A | p.Arg518His | p.R518H | Q9P2Q2 | protein_coding | deleterious(0) | possibly_damaging(0.908) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| FRMD4A | SNV | Missense_Mutation | c.637C>G | p.Leu213Val | p.L213V | Q9P2Q2 | protein_coding | deleterious(0.04) | possibly_damaging(0.842) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| FRMD4A | SNV | Missense_Mutation | c.185N>A | p.Gly62Glu | p.G62E | Q9P2Q2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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