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Gene: LAMB4 |
Gene summary for LAMB4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LAMB4 | Gene ID | 22798 |
Gene name | laminin subunit beta 4 | |
Gene Alias | LAMB4 | |
Cytomap | 7q31.1 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A4D0S4 |
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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 |
22798 | LAMB4 | P4_S8_cSCC | Human | Skin | cSCC | 2.20e-38 | 7.42e-01 | -0.3095 |
22798 | LAMB4 | P1_cSCC | Human | Skin | cSCC | 1.06e-15 | 5.97e-01 | 0.0292 |
22798 | LAMB4 | P2_cSCC | Human | Skin | cSCC | 2.43e-06 | 2.45e-01 | -0.024 |
22798 | LAMB4 | P4_cSCC | Human | Skin | cSCC | 1.75e-05 | 2.13e-01 | -0.00290000000000005 |
22798 | LAMB4 | cSCC_p1 | Human | Skin | cSCC | 1.87e-06 | 3.05e-01 | -0.1916 |
22798 | LAMB4 | cSCC_p11 | Human | Skin | cSCC | 9.03e-08 | 3.29e-01 | -0.2102 |
22798 | LAMB4 | cSCC_p4 | Human | Skin | cSCC | 6.75e-13 | 3.60e-01 | -0.2022 |
22798 | LAMB4 | cSCC_p6 | Human | Skin | cSCC | 2.27e-05 | 2.23e-01 | -0.1989 |
22798 | LAMB4 | cSCC_p7 | Human | Skin | cSCC | 1.85e-02 | 2.76e-01 | -0.2332 |
22798 | LAMB4 | cSCC_p8 | Human | Skin | cSCC | 4.01e-10 | 2.40e-01 | -0.1971 |
22798 | LAMB4 | cSCC_p9 | Human | Skin | cSCC | 1.99e-11 | 2.52e-01 | -0.1991 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003158926 | Skin | cSCC | cell-substrate adhesion | 130/4864 | 363/18723 | 1.87e-05 | 2.23e-04 | 130 |
GO:0034446110 | Skin | cSCC | substrate adhesion-dependent cell spreading | 43/4864 | 108/18723 | 1.12e-03 | 7.36e-03 | 43 |
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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 |
LAMB4 | SNV | Missense_Mutation | c.860N>A | p.Pro287His | p.P287H | A4D0S4 | protein_coding | tolerated(0.22) | benign(0.146) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
LAMB4 | SNV | Missense_Mutation | rs755935994 | c.3575N>T | p.Ala1192Val | p.A1192V | A4D0S4 | protein_coding | tolerated(0.23) | benign(0.001) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LAMB4 | SNV | Missense_Mutation | novel | c.4147N>T | p.Pro1383Ser | p.P1383S | A4D0S4 | protein_coding | tolerated(0.29) | benign(0.012) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LAMB4 | SNV | Missense_Mutation | novel | c.1336N>A | p.Ala446Thr | p.A446T | A4D0S4 | protein_coding | deleterious(0.03) | possibly_damaging(0.793) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LAMB4 | SNV | Missense_Mutation | c.1180N>T | p.Pro394Ser | p.P394S | A4D0S4 | protein_coding | tolerated(0.13) | probably_damaging(0.946) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LAMB4 | SNV | Missense_Mutation | novel | c.992N>T | p.Ser331Leu | p.S331L | A4D0S4 | protein_coding | tolerated(0.26) | benign(0.006) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LAMB4 | SNV | Missense_Mutation | rs779949946 | c.911N>T | p.Pro304Leu | p.P304L | A4D0S4 | protein_coding | tolerated(1) | benign(0.007) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
LAMB4 | SNV | Missense_Mutation | rs375377087 | c.4871G>A | p.Arg1624Gln | p.R1624Q | A4D0S4 | protein_coding | tolerated(1) | benign(0) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
LAMB4 | SNV | Missense_Mutation | rs753185686 | c.3832G>A | p.Ala1278Thr | p.A1278T | A4D0S4 | protein_coding | tolerated(0.32) | benign(0) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
LAMB4 | SNV | Missense_Mutation | rs767544532 | c.2868C>A | p.Phe956Leu | p.F956L | A4D0S4 | protein_coding | deleterious(0.01) | probably_damaging(0.983) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | 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 |
22798 | LAMB4 | DRUGGABLE GENOME | CHEMBL2095222 | OCRIPLASMIN |
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