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Gene: LAMA1 |
Gene summary for LAMA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LAMA1 | Gene ID | 284217 |
| Gene name | laminin subunit alpha 1 | |
| Gene Alias | LAMA | |
| Cytomap | 18p11.31 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | P25391 |
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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 |
| 284217 | LAMA1 | AEH-subject3 | Human | Endometrium | AEH | 4.09e-18 | 5.42e-01 | -0.2576 |
| 284217 | LAMA1 | AEH-subject5 | Human | Endometrium | AEH | 4.95e-15 | 5.41e-01 | -0.2953 |
| 284217 | LAMA1 | EEC-subject1 | Human | Endometrium | EEC | 3.16e-09 | 3.86e-01 | -0.2682 |
| 284217 | LAMA1 | EEC-subject2 | Human | Endometrium | EEC | 5.02e-12 | 3.82e-01 | -0.2607 |
| 284217 | LAMA1 | EEC-subject5 | Human | Endometrium | EEC | 5.80e-08 | 3.72e-01 | -0.249 |
| 284217 | LAMA1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 6.26e-04 | 5.60e-03 | -0.1883 |
| 284217 | LAMA1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 4.00e-09 | 4.00e-01 | -0.1934 |
| 284217 | LAMA1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 4.14e-03 | -1.83e-03 | -0.1916 |
| 284217 | LAMA1 | P2T-E | Human | Esophagus | ESCC | 1.53e-19 | 3.30e-01 | 0.1177 |
| 284217 | LAMA1 | P4T-E | Human | Esophagus | ESCC | 2.45e-12 | 3.10e-01 | 0.1323 |
| 284217 | LAMA1 | P5T-E | Human | Esophagus | ESCC | 2.28e-35 | 5.69e-01 | 0.1327 |
| 284217 | LAMA1 | P11T-E | Human | Esophagus | ESCC | 1.20e-09 | 4.28e-01 | 0.1426 |
| 284217 | LAMA1 | P12T-E | Human | Esophagus | ESCC | 3.87e-34 | 6.73e-01 | 0.1122 |
| 284217 | LAMA1 | P15T-E | Human | Esophagus | ESCC | 1.67e-14 | 3.46e-01 | 0.1149 |
| 284217 | LAMA1 | P22T-E | Human | Esophagus | ESCC | 1.13e-16 | 3.79e-01 | 0.1236 |
| 284217 | LAMA1 | P26T-E | Human | Esophagus | ESCC | 2.39e-24 | 4.16e-01 | 0.1276 |
| 284217 | LAMA1 | P31T-E | Human | Esophagus | ESCC | 1.23e-20 | 4.85e-01 | 0.1251 |
| 284217 | LAMA1 | P32T-E | Human | Esophagus | ESCC | 2.06e-08 | 2.00e-01 | 0.1666 |
| 284217 | LAMA1 | P37T-E | Human | Esophagus | ESCC | 3.50e-19 | 4.50e-01 | 0.1371 |
| 284217 | LAMA1 | P42T-E | Human | Esophagus | ESCC | 2.79e-04 | 1.52e-01 | 0.1175 |
| Page: 1 2 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:000716310 | Endometrium | AEH | establishment or maintenance of cell polarity | 54/2100 | 218/18723 | 1.30e-08 | 8.47e-07 | 54 |
| 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:004873216 | Endometrium | AEH | gland development | 83/2100 | 436/18723 | 8.62e-07 | 3.11e-05 | 83 |
| GO:00300109 | Endometrium | AEH | establishment of cell polarity | 36/2100 | 143/18723 | 2.19e-06 | 6.49e-05 | 36 |
| GO:00605627 | Endometrium | AEH | epithelial tube morphogenesis | 63/2100 | 325/18723 | 9.63e-06 | 2.23e-04 | 63 |
| GO:00226129 | Endometrium | AEH | gland morphogenesis | 30/2100 | 118/18723 | 1.21e-05 | 2.68e-04 | 30 |
| GO:00611384 | Endometrium | AEH | morphogenesis of a branching epithelium | 40/2100 | 182/18723 | 2.16e-05 | 4.20e-04 | 40 |
| GO:00017637 | Endometrium | AEH | morphogenesis of a branching structure | 42/2100 | 196/18723 | 2.58e-05 | 4.86e-04 | 42 |
| GO:00487542 | Endometrium | AEH | branching morphogenesis of an epithelial tube | 33/2100 | 151/18723 | 1.22e-04 | 1.68e-03 | 33 |
| GO:00459956 | Endometrium | AEH | regulation of embryonic development | 18/2100 | 64/18723 | 1.65e-04 | 2.15e-03 | 18 |
| GO:00350886 | Endometrium | AEH | establishment or maintenance of apical/basal cell polarity | 14/2100 | 49/18723 | 7.19e-04 | 6.90e-03 | 14 |
| GO:00612456 | Endometrium | AEH | establishment or maintenance of bipolar cell polarity | 14/2100 | 49/18723 | 7.19e-04 | 6.90e-03 | 14 |
| GO:00451976 | Endometrium | AEH | establishment or maintenance of epithelial cell apical/basal polarity | 13/2100 | 44/18723 | 7.79e-04 | 7.36e-03 | 13 |
| GO:00901628 | Endometrium | AEH | establishment of epithelial cell polarity | 10/2100 | 31/18723 | 1.48e-03 | 1.23e-02 | 10 |
| GO:00605414 | Endometrium | AEH | respiratory system development | 37/2100 | 203/18723 | 1.97e-03 | 1.54e-02 | 37 |
| GO:00303246 | Endometrium | AEH | lung development | 33/2100 | 177/18723 | 2.30e-03 | 1.74e-02 | 33 |
| GO:00604254 | Endometrium | AEH | lung morphogenesis | 13/2100 | 50/18723 | 2.81e-03 | 2.02e-02 | 13 |
| GO:00303236 | Endometrium | AEH | respiratory tube development | 33/2100 | 181/18723 | 3.33e-03 | 2.32e-02 | 33 |
| GO:00017385 | Endometrium | AEH | morphogenesis of a polarized epithelium | 20/2100 | 94/18723 | 3.44e-03 | 2.38e-02 | 20 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| hsa0514632 | Endometrium | EEC | Amoebiasis | 28/1237 | 102/8465 | 5.23e-04 | 3.83e-03 | 2.85e-03 | 28 |
| hsa0514517 | Endometrium | EEC | Toxoplasmosis | 28/1237 | 112/8465 | 2.48e-03 | 1.48e-02 | 1.11e-02 | 28 |
| hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
| hsa052229 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
| hsa0451020 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
| hsa0522216 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
| Page: 1 2 |
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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 |
| LAMA1 | SNV | Missense_Mutation | novel | c.1082N>A | p.Cys361Tyr | p.C361Y | P25391 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-3C-AALK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
| LAMA1 | SNV | Missense_Mutation | novel | c.1870N>A | p.Glu624Lys | p.E624K | P25391 | protein_coding | tolerated(0.21) | possibly_damaging(0.516) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| LAMA1 | SNV | Missense_Mutation | c.1211N>T | p.Ser404Phe | p.S404F | P25391 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-A2-A25D-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| LAMA1 | SNV | Missense_Mutation | novel | c.3229T>G | p.Cys1077Gly | p.C1077G | P25391 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A4S3-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAMA1 | SNV | Missense_Mutation | c.3025N>T | p.Pro1009Ser | p.P1009S | P25391 | protein_coding | tolerated(0.09) | possibly_damaging(0.671) | TCGA-A8-A07O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | ||
| LAMA1 | SNV | Missense_Mutation | novel | c.8473N>A | p.Gly2825Arg | p.G2825R | P25391 | protein_coding | deleterious(0.01) | probably_damaging(0.973) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| LAMA1 | SNV | Missense_Mutation | c.484C>G | p.Arg162Gly | p.R162G | P25391 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LAMA1 | SNV | Missense_Mutation | novel | c.8971C>G | p.Leu2991Val | p.L2991V | P25391 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-AC-A2QI-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | CR |
| LAMA1 | SNV | Missense_Mutation | rs756248044 | c.7609N>T | p.Arg2537Cys | p.R2537C | P25391 | protein_coding | deleterious(0) | possibly_damaging(0.765) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LAMA1 | SNV | Missense_Mutation | rs777131128 | c.6383N>A | p.Arg2128Gln | p.R2128Q | P25391 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 |
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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 |
| 284217 | LAMA1 | DRUGGABLE GENOME | CHEMBL2095222 | OCRIPLASMIN |
| Page: 1 |
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