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Gene: LAMA2 |
Gene summary for LAMA2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LAMA2 | Gene ID | 3908 |
Gene name | laminin subunit alpha 2 | |
Gene Alias | LAMM | |
Cytomap | 6q22.33 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | P24043 |
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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 |
3908 | LAMA2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 9.77e-03 | 1.74e-01 | -0.0811 |
3908 | LAMA2 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.87e-04 | 1.85e-01 | -0.1088 |
3908 | LAMA2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.84e-03 | 1.70e-01 | -0.1954 |
3908 | LAMA2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.02e-03 | 1.60e-01 | -0.059 |
3908 | LAMA2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.21e-02 | 2.41e-01 | 0.0338 |
3908 | LAMA2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.82e-02 | 1.72e-01 | 0.0588 |
3908 | LAMA2 | A001-C-007 | Human | Colorectum | CRC | 1.31e-11 | 6.41e-01 | 0.1899 |
3908 | LAMA2 | CRC-1-8810 | Human | Colorectum | CRC | 2.71e-19 | 6.53e-01 | 0.6257 |
3908 | LAMA2 | AEH-subject1 | Human | Endometrium | AEH | 9.64e-03 | -1.52e-01 | -0.3059 |
3908 | LAMA2 | AEH-subject2 | Human | Endometrium | AEH | 6.09e-04 | -1.53e-01 | -0.2525 |
3908 | LAMA2 | AEH-subject5 | Human | Endometrium | AEH | 6.55e-20 | 6.88e-01 | -0.2953 |
3908 | LAMA2 | EEC-subject1 | Human | Endometrium | EEC | 4.88e-05 | -1.62e-01 | -0.2682 |
3908 | LAMA2 | EEC-subject2 | Human | Endometrium | EEC | 1.07e-03 | -1.79e-01 | -0.2607 |
3908 | LAMA2 | EEC-subject3 | Human | Endometrium | EEC | 2.80e-04 | -1.24e-01 | -0.2525 |
3908 | LAMA2 | EEC-subject4 | Human | Endometrium | EEC | 3.57e-12 | 6.45e-01 | -0.2571 |
3908 | LAMA2 | EEC-subject5 | Human | Endometrium | EEC | 1.63e-07 | -1.80e-01 | -0.249 |
3908 | LAMA2 | GSM5276935 | Human | Endometrium | EEC | 8.77e-08 | -1.73e-01 | -0.123 |
3908 | LAMA2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.30e-06 | -1.87e-01 | -0.1869 |
3908 | LAMA2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 1.28e-05 | -1.87e-01 | -0.1875 |
3908 | LAMA2 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.66e-05 | -1.73e-01 | -0.1883 |
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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:0007409 | Colorectum | AD | axonogenesis | 122/3918 | 418/18723 | 3.36e-05 | 6.15e-04 | 122 |
GO:0061564 | Colorectum | AD | axon development | 132/3918 | 467/18723 | 8.40e-05 | 1.31e-03 | 132 |
GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
GO:0001894 | Colorectum | AD | tissue homeostasis | 81/3918 | 268/18723 | 1.96e-04 | 2.62e-03 | 81 |
GO:0045995 | Colorectum | AD | regulation of embryonic development | 24/3918 | 64/18723 | 1.72e-03 | 1.43e-02 | 24 |
GO:0007411 | Colorectum | AD | axon guidance | 64/3918 | 227/18723 | 5.41e-03 | 3.55e-02 | 64 |
GO:0097485 | Colorectum | AD | neuron projection guidance | 64/3918 | 228/18723 | 6.02e-03 | 3.78e-02 | 64 |
GO:0035633 | Colorectum | AD | maintenance of blood-brain barrier | 14/3918 | 35/18723 | 7.92e-03 | 4.73e-02 | 14 |
GO:00074094 | Colorectum | CRC | axonogenesis | 81/2078 | 418/18723 | 3.60e-07 | 2.99e-05 | 81 |
GO:00615644 | Colorectum | CRC | axon development | 86/2078 | 467/18723 | 1.48e-06 | 8.12e-05 | 86 |
GO:00602495 | Colorectum | CRC | anatomical structure homeostasis | 57/2078 | 314/18723 | 1.24e-04 | 2.41e-03 | 57 |
GO:00018945 | Colorectum | CRC | tissue homeostasis | 48/2078 | 268/18723 | 5.56e-04 | 7.70e-03 | 48 |
GO:0050804 | Colorectum | CRC | modulation of chemical synaptic transmission | 70/2078 | 439/18723 | 1.15e-03 | 1.33e-02 | 70 |
GO:0099177 | Colorectum | CRC | regulation of trans-synaptic signaling | 70/2078 | 440/18723 | 1.23e-03 | 1.38e-02 | 70 |
GO:00074098 | Endometrium | AEH | axonogenesis | 81/2100 | 418/18723 | 5.54e-07 | 2.12e-05 | 81 |
GO:00615648 | Endometrium | AEH | axon development | 88/2100 | 467/18723 | 6.39e-07 | 2.38e-05 | 88 |
GO:00356337 | Endometrium | AEH | maintenance of blood-brain barrier | 14/2100 | 35/18723 | 1.12e-05 | 2.52e-04 | 14 |
GO:00075174 | Endometrium | AEH | muscle organ development | 60/2100 | 327/18723 | 8.19e-05 | 1.22e-03 | 60 |
GO:00459956 | Endometrium | AEH | regulation of embryonic development | 18/2100 | 64/18723 | 1.65e-04 | 2.15e-03 | 18 |
GO:000189410 | Endometrium | AEH | tissue homeostasis | 50/2100 | 268/18723 | 2.04e-04 | 2.54e-03 | 50 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04510 | Colorectum | AD | Focal adhesion | 67/2092 | 203/8465 | 4.40e-03 | 2.17e-02 | 1.38e-02 | 67 |
hsa045101 | Colorectum | AD | Focal adhesion | 67/2092 | 203/8465 | 4.40e-03 | 2.17e-02 | 1.38e-02 | 67 |
hsa045104 | Colorectum | CRC | Focal adhesion | 51/1091 | 203/8465 | 1.29e-06 | 5.41e-05 | 3.66e-05 | 51 |
hsa041512 | Colorectum | CRC | PI3K-Akt signaling pathway | 64/1091 | 354/8465 | 2.70e-03 | 1.77e-02 | 1.20e-02 | 64 |
hsa054122 | Colorectum | CRC | Arrhythmogenic right ventricular cardiomyopathy | 18/1091 | 77/8465 | 7.90e-03 | 3.77e-02 | 2.55e-02 | 18 |
hsa045105 | Colorectum | CRC | Focal adhesion | 51/1091 | 203/8465 | 1.29e-06 | 5.41e-05 | 3.66e-05 | 51 |
hsa041513 | Colorectum | CRC | PI3K-Akt signaling pathway | 64/1091 | 354/8465 | 2.70e-03 | 1.77e-02 | 1.20e-02 | 64 |
hsa054123 | Colorectum | CRC | Arrhythmogenic right ventricular cardiomyopathy | 18/1091 | 77/8465 | 7.90e-03 | 3.77e-02 | 2.55e-02 | 18 |
hsa0541625 | Endometrium | AEH | Viral myocarditis | 27/1197 | 60/8465 | 6.98e-09 | 1.13e-07 | 8.30e-08 | 27 |
hsa0451015 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa051466 | Endometrium | AEH | Amoebiasis | 29/1197 | 102/8465 | 1.22e-04 | 1.10e-03 | 8.06e-04 | 29 |
hsa05416111 | Endometrium | AEH | Viral myocarditis | 27/1197 | 60/8465 | 6.98e-09 | 1.13e-07 | 8.30e-08 | 27 |
hsa0451016 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa0514613 | Endometrium | AEH | Amoebiasis | 29/1197 | 102/8465 | 1.22e-04 | 1.10e-03 | 8.06e-04 | 29 |
hsa0541626 | Endometrium | EEC | Viral myocarditis | 28/1237 | 60/8465 | 2.81e-09 | 5.77e-08 | 4.30e-08 | 28 |
hsa0451024 | Endometrium | EEC | Focal adhesion | 58/1237 | 203/8465 | 1.61e-07 | 2.30e-06 | 1.71e-06 | 58 |
hsa0514622 | Endometrium | EEC | Amoebiasis | 28/1237 | 102/8465 | 5.23e-04 | 3.83e-03 | 2.85e-03 | 28 |
hsa0514516 | Endometrium | EEC | Toxoplasmosis | 28/1237 | 112/8465 | 2.48e-03 | 1.48e-02 | 1.11e-02 | 28 |
hsa0541635 | Endometrium | EEC | Viral myocarditis | 28/1237 | 60/8465 | 2.81e-09 | 5.77e-08 | 4.30e-08 | 28 |
hsa0451034 | Endometrium | EEC | Focal adhesion | 58/1237 | 203/8465 | 1.61e-07 | 2.30e-06 | 1.71e-06 | 58 |
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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 |
LAMA2 | ITGA1_ITGB1 | LAMA2_ITGA1_ITGB1 | LAMININ | Breast | ADJ |
LAMA2 | ITGA2_ITGB1 | LAMA2_ITGA2_ITGB1 | LAMININ | Breast | ADJ |
LAMA2 | CD44 | LAMA2_CD44 | LAMININ | Breast | ADJ |
LAMA2 | ITGA1_ITGB1 | LAMA2_ITGA1_ITGB1 | LAMININ | Breast | DCIS |
LAMA2 | ITGA2_ITGB1 | LAMA2_ITGA2_ITGB1 | LAMININ | Breast | DCIS |
LAMA2 | ITGA6_ITGB1 | LAMA2_ITGA6_ITGB1 | LAMININ | Breast | DCIS |
LAMA2 | ITGA7_ITGB1 | LAMA2_ITGA7_ITGB1 | LAMININ | Breast | DCIS |
LAMA2 | ITGA6_ITGB4 | LAMA2_ITGA6_ITGB4 | LAMININ | Breast | DCIS |
LAMA2 | CD44 | LAMA2_CD44 | LAMININ | Breast | DCIS |
LAMA2 | DAG1 | LAMA2_DAG1 | LAMININ | Breast | DCIS |
LAMA2 | ITGA1_ITGB1 | LAMA2_ITGA1_ITGB1 | LAMININ | Breast | Healthy |
LAMA2 | ITGA2_ITGB1 | LAMA2_ITGA2_ITGB1 | LAMININ | Breast | Healthy |
LAMA2 | ITGA6_ITGB1 | LAMA2_ITGA6_ITGB1 | LAMININ | Breast | Healthy |
LAMA2 | ITGA7_ITGB1 | LAMA2_ITGA7_ITGB1 | LAMININ | Breast | Healthy |
LAMA2 | ITGAV_ITGB8 | LAMA2_ITGAV_ITGB8 | LAMININ | Breast | Healthy |
LAMA2 | CD44 | LAMA2_CD44 | LAMININ | Breast | Healthy |
LAMA2 | ITGA1_ITGB1 | LAMA2_ITGA1_ITGB1 | LAMININ | Cervix | ADJ |
LAMA2 | ITGA2_ITGB1 | LAMA2_ITGA2_ITGB1 | LAMININ | Cervix | ADJ |
LAMA2 | ITGA3_ITGB1 | LAMA2_ITGA3_ITGB1 | LAMININ | Cervix | ADJ |
LAMA2 | ITGA6_ITGB1 | LAMA2_ITGA6_ITGB1 | LAMININ | Cervix | ADJ |
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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 |
LAMA2 | SNV | Missense_Mutation | c.7679N>T | p.Ser2560Phe | p.S2560F | P24043 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
LAMA2 | SNV | Missense_Mutation | c.6413N>A | p.Arg2138Gln | p.R2138Q | P24043 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CG-5726-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LAMA2 | SNV | Missense_Mutation | novel | c.8342N>A | p.Thr2781Asn | p.T2781N | P24043 | protein_coding | tolerated(0.23) | benign(0.342) | TCGA-D7-6521-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | plfe/flo | PD |
LAMA2 | SNV | Missense_Mutation | novel | c.3578C>A | p.Thr1193Asn | p.T1193N | P24043 | protein_coding | tolerated(0.2) | possibly_damaging(0.501) | TCGA-D7-6528-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LAMA2 | SNV | Missense_Mutation | rs376585927 | c.5813C>T | p.Ala1938Val | p.A1938V | P24043 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-EQ-A4SO-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR |
LAMA2 | SNV | Missense_Mutation | c.809N>A | p.Val270Asp | p.V270D | P24043 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
LAMA2 | SNV | Missense_Mutation | c.4282N>A | p.Leu1428Met | p.L1428M | P24043 | protein_coding | tolerated(0.27) | benign(0.012) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
LAMA2 | SNV | Missense_Mutation | rs368316367 | c.5932C>A | p.Leu1978Ile | p.L1978I | P24043 | protein_coding | deleterious(0.01) | benign(0.355) | TCGA-HU-A4GH-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LAMA2 | SNV | Missense_Mutation | rs150691000 | c.5531N>A | p.Arg1844His | p.R1844H | P24043 | protein_coding | tolerated(0.13) | benign(0.003) | TCGA-HU-A4H6-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | doxifluridine | SD |
LAMA2 | SNV | Missense_Mutation | c.7003N>A | p.Glu2335Lys | p.E2335K | P24043 | protein_coding | deleterious(0.03) | benign(0.108) | TCGA-SW-A7EA-01 | Stomach | stomach adenocarcinoma | Female | <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 |
3908 | LAMA2 | DRUGGABLE GENOME | CHEMBL2095222 | OCRIPLASMIN |
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