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Gene: FRMD4B |
Gene summary for FRMD4B |
Gene summary. |
Gene information | Species | Human | Gene symbol | FRMD4B | Gene ID | 23150 |
Gene name | FERM domain containing 4B | |
Gene Alias | 6030440G05Rik | |
Cytomap | 3p14.1 | |
Gene Type | protein-coding | GO ID | GO:0007163 | UniProtAcc | B3KNA2 |
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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 |
23150 | FRMD4B | LZE4T | Human | Esophagus | ESCC | 3.80e-11 | 7.17e-01 | 0.0811 |
23150 | FRMD4B | LZE5T | Human | Esophagus | ESCC | 1.61e-02 | 9.53e-02 | 0.0514 |
23150 | FRMD4B | LZE7T | Human | Esophagus | ESCC | 6.26e-03 | 3.51e-01 | 0.0667 |
23150 | FRMD4B | LZE8T | Human | Esophagus | ESCC | 9.93e-04 | 7.32e-02 | 0.067 |
23150 | FRMD4B | LZE24T | Human | Esophagus | ESCC | 2.32e-02 | 3.21e-01 | 0.0596 |
23150 | FRMD4B | P1T-E | Human | Esophagus | ESCC | 1.03e-06 | 3.57e-01 | 0.0875 |
23150 | FRMD4B | P2T-E | Human | Esophagus | ESCC | 3.93e-27 | 5.81e-01 | 0.1177 |
23150 | FRMD4B | P4T-E | Human | Esophagus | ESCC | 1.23e-13 | 5.90e-01 | 0.1323 |
23150 | FRMD4B | P5T-E | Human | Esophagus | ESCC | 1.00e-10 | 3.07e-01 | 0.1327 |
23150 | FRMD4B | P8T-E | Human | Esophagus | ESCC | 1.81e-13 | 3.05e-01 | 0.0889 |
23150 | FRMD4B | P9T-E | Human | Esophagus | ESCC | 4.41e-12 | 5.08e-01 | 0.1131 |
23150 | FRMD4B | P10T-E | Human | Esophagus | ESCC | 8.32e-27 | 5.88e-01 | 0.116 |
23150 | FRMD4B | P11T-E | Human | Esophagus | ESCC | 8.22e-08 | 3.14e-01 | 0.1426 |
23150 | FRMD4B | P12T-E | Human | Esophagus | ESCC | 2.20e-36 | 7.43e-01 | 0.1122 |
23150 | FRMD4B | P15T-E | Human | Esophagus | ESCC | 5.72e-09 | 3.00e-01 | 0.1149 |
23150 | FRMD4B | P16T-E | Human | Esophagus | ESCC | 3.02e-16 | 1.45e-01 | 0.1153 |
23150 | FRMD4B | P17T-E | Human | Esophagus | ESCC | 3.30e-03 | 2.57e-01 | 0.1278 |
23150 | FRMD4B | P20T-E | Human | Esophagus | ESCC | 9.10e-04 | 8.93e-02 | 0.1124 |
23150 | FRMD4B | P21T-E | Human | Esophagus | ESCC | 1.88e-10 | 3.19e-01 | 0.1617 |
23150 | FRMD4B | P22T-E | Human | Esophagus | ESCC | 4.48e-19 | -2.31e-02 | 0.1236 |
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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:000716320 | Esophagus | ESCC | establishment or maintenance of cell polarity | 143/8552 | 218/18723 | 2.05e-09 | 4.65e-08 | 143 |
GO:003001018 | Esophagus | ESCC | establishment of cell polarity | 96/8552 | 143/18723 | 1.69e-07 | 2.67e-06 | 96 |
GO:009016216 | Esophagus | ESCC | establishment of epithelial cell polarity | 25/8552 | 31/18723 | 7.13e-05 | 5.38e-04 | 25 |
GO:000716312 | Liver | Cirrhotic | establishment or maintenance of cell polarity | 82/4634 | 218/18723 | 1.55e-05 | 2.11e-04 | 82 |
GO:00901625 | Liver | Cirrhotic | establishment of epithelial cell polarity | 14/4634 | 31/18723 | 1.05e-02 | 4.65e-02 | 14 |
GO:003001012 | Liver | Cirrhotic | establishment of cell polarity | 48/4634 | 143/18723 | 1.09e-02 | 4.79e-02 | 48 |
GO:000716322 | Liver | HCC | establishment or maintenance of cell polarity | 133/7958 | 218/18723 | 2.48e-08 | 5.73e-07 | 133 |
GO:003001022 | Liver | HCC | establishment of cell polarity | 82/7958 | 143/18723 | 2.38e-04 | 1.79e-03 | 82 |
GO:00071637 | Lung | IAC | establishment or maintenance of cell polarity | 61/2061 | 218/18723 | 3.10e-12 | 3.07e-09 | 61 |
GO:00300107 | Lung | IAC | establishment of cell polarity | 46/2061 | 143/18723 | 7.70e-12 | 4.27e-09 | 46 |
GO:00901626 | Lung | IAC | establishment of epithelial cell polarity | 11/2061 | 31/18723 | 2.91e-04 | 4.72e-03 | 11 |
GO:000716313 | Lung | AIS | establishment or maintenance of cell polarity | 56/1849 | 218/18723 | 1.31e-11 | 6.13e-09 | 56 |
GO:003001013 | Lung | AIS | establishment of cell polarity | 42/1849 | 143/18723 | 5.03e-11 | 1.95e-08 | 42 |
GO:009016212 | Lung | AIS | establishment of epithelial cell polarity | 11/1849 | 31/18723 | 1.10e-04 | 2.57e-03 | 11 |
GO:000716323 | Lung | AAH | establishment or maintenance of cell polarity | 24/613 | 218/18723 | 2.21e-07 | 1.01e-04 | 24 |
GO:003001023 | Lung | AAH | establishment of cell polarity | 17/613 | 143/18723 | 4.53e-06 | 1.22e-03 | 17 |
GO:009016222 | Lung | AAH | establishment of epithelial cell polarity | 6/613 | 31/18723 | 4.40e-04 | 1.92e-02 | 6 |
GO:003001031 | Lung | MIAC | establishment of cell polarity | 27/967 | 143/18723 | 4.16e-09 | 4.27e-06 | 27 |
GO:000716332 | Lung | MIAC | establishment or maintenance of cell polarity | 34/967 | 218/18723 | 7.70e-09 | 4.94e-06 | 34 |
GO:009016231 | Lung | MIAC | establishment of epithelial cell polarity | 7/967 | 31/18723 | 8.47e-04 | 1.83e-02 | 7 |
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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 |
FRMD4B | SNV | Missense_Mutation | novel | c.1837N>T | p.Pro613Ser | p.P613S | Q9Y2L6 | protein_coding | tolerated(0.08) | benign(0.056) | TCGA-43-2576-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
FRMD4B | SNV | Missense_Mutation | rs533947293 | c.2699G>T | p.Arg900Leu | p.R900L | Q9Y2L6 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-56-6545-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
FRMD4B | SNV | Missense_Mutation | rs533947293 | c.2699G>T | p.Arg900Leu | p.R900L | Q9Y2L6 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-63-A5MS-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
FRMD4B | SNV | Missense_Mutation | novel | c.3062G>T | p.Arg1021Ile | p.R1021I | Q9Y2L6 | protein_coding | deleterious_low_confidence(0.05) | benign(0.001) | TCGA-98-A538-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
FRMD4B | deletion | Frame_Shift_Del | novel | c.3069_3070delNN | p.Phe1023LeufsTer3 | p.F1023Lfs*3 | Q9Y2L6 | protein_coding | TCGA-77-7335-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
FRMD4B | SNV | Missense_Mutation | c.1768N>A | p.Asp590Asn | p.D590N | Q9Y2L6 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-CR-7374-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
FRMD4B | SNV | Missense_Mutation | novel | c.1795N>T | p.Gly599Trp | p.G599W | Q9Y2L6 | protein_coding | tolerated(0.05) | possibly_damaging(0.514) | TCGA-D6-6825-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
FRMD4B | SNV | Missense_Mutation | rs373504856 | c.1967N>A | p.Arg656Gln | p.R656Q | Q9Y2L6 | protein_coding | tolerated(0.81) | benign(0) | TCGA-CD-A4MG-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
FRMD4B | SNV | Missense_Mutation | rs376555402 | c.2698N>T | p.Arg900Cys | p.R900C | Q9Y2L6 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-HJ-7597-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | CR |
FRMD4B | SNV | Missense_Mutation | rs750455183 | c.1880N>T | p.Ser627Leu | p.S627L | Q9Y2L6 | protein_coding | deleterious(0.03) | benign(0.093) | TCGA-HU-A4GF-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | 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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