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Gene: LARP1 |
Gene summary for LARP1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LARP1 | Gene ID | 23367 |
Gene name | La ribonucleoprotein 1, translational regulator | |
Gene Alias | LARP | |
Cytomap | 5q33.2 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q6PKG0 |
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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 |
23367 | LARP1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.37e-03 | 4.87e-01 | -0.0811 |
23367 | LARP1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.05e-03 | 4.92e-01 | -0.1088 |
23367 | LARP1 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.11e-12 | 6.29e-01 | -0.1954 |
23367 | LARP1 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.15e-03 | 5.06e-01 | -0.1464 |
23367 | LARP1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.95e-11 | 8.97e-01 | -0.059 |
23367 | LARP1 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.23e-05 | 5.24e-01 | 0.096 |
23367 | LARP1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.17e-10 | 6.67e-01 | 0.0674 |
23367 | LARP1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.68e-04 | 5.65e-01 | 0.0588 |
23367 | LARP1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.18e-03 | 5.42e-01 | 0.294 |
23367 | LARP1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 7.39e-04 | 9.34e-01 | 0.3487 |
23367 | LARP1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.86e-15 | 9.57e-01 | 0.281 |
23367 | LARP1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 8.25e-22 | 1.24e+00 | 0.3859 |
23367 | LARP1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 6.64e-08 | 8.32e-01 | 0.2585 |
23367 | LARP1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.71e-09 | 6.54e-01 | 0.3005 |
23367 | LARP1 | A002-C-010 | Human | Colorectum | FAP | 5.27e-04 | -2.20e-01 | 0.242 |
23367 | LARP1 | A001-C-207 | Human | Colorectum | FAP | 1.14e-02 | -2.28e-01 | 0.1278 |
23367 | LARP1 | A015-C-203 | Human | Colorectum | FAP | 1.03e-26 | -2.32e-01 | -0.1294 |
23367 | LARP1 | A015-C-204 | Human | Colorectum | FAP | 1.51e-04 | -4.75e-02 | -0.0228 |
23367 | LARP1 | A014-C-040 | Human | Colorectum | FAP | 1.13e-04 | -3.53e-01 | -0.1184 |
23367 | LARP1 | A002-C-201 | Human | Colorectum | FAP | 2.96e-11 | -9.23e-02 | 0.0324 |
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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:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
GO:0009896 | Colorectum | AD | positive regulation of catabolic process | 180/3918 | 492/18723 | 4.33e-16 | 1.94e-13 | 180 |
GO:1903311 | Colorectum | AD | regulation of mRNA metabolic process | 117/3918 | 288/18723 | 1.69e-14 | 4.23e-12 | 117 |
GO:0031331 | Colorectum | AD | positive regulation of cellular catabolic process | 156/3918 | 427/18723 | 4.68e-14 | 1.05e-11 | 156 |
GO:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
GO:0019058 | Colorectum | AD | viral life cycle | 119/3918 | 317/18723 | 6.18e-12 | 8.23e-10 | 119 |
GO:0006401 | Colorectum | AD | RNA catabolic process | 102/3918 | 278/18723 | 8.64e-10 | 6.76e-08 | 102 |
GO:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
GO:0006402 | Colorectum | AD | mRNA catabolic process | 87/3918 | 232/18723 | 4.40e-09 | 2.84e-07 | 87 |
GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
GO:0034655 | Colorectum | AD | nucleobase-containing compound catabolic process | 133/3918 | 407/18723 | 1.56e-08 | 9.12e-07 | 133 |
GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
GO:0061013 | Colorectum | AD | regulation of mRNA catabolic process | 64/3918 | 166/18723 | 1.44e-07 | 6.59e-06 | 64 |
GO:0043487 | Colorectum | AD | regulation of RNA stability | 63/3918 | 170/18723 | 9.17e-07 | 3.12e-05 | 63 |
GO:0006417 | Colorectum | AD | regulation of translation | 141/3918 | 468/18723 | 1.32e-06 | 4.22e-05 | 141 |
GO:0048524 | Colorectum | AD | positive regulation of viral process | 31/3918 | 65/18723 | 1.33e-06 | 4.23e-05 | 31 |
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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 |
∗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 |
LARP1 | SNV | Missense_Mutation | novel | c.1289C>T | p.Pro430Leu | p.P430L | Q6PKG0 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-21-1079-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
LARP1 | SNV | Missense_Mutation | novel | c.2227A>T | p.Thr743Ser | p.T743S | Q6PKG0 | protein_coding | deleterious(0.01) | probably_damaging(0.966) | TCGA-22-1016-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LARP1 | SNV | Missense_Mutation | novel | c.2732N>G | p.Tyr911Cys | p.Y911C | Q6PKG0 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-37-A5EL-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | temodal | PD |
LARP1 | SNV | Missense_Mutation | novel | c.2765N>T | p.Tyr922Phe | p.Y922F | Q6PKG0 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-43-8118-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
LARP1 | SNV | Missense_Mutation | c.2081T>C | p.Val694Ala | p.V694A | Q6PKG0 | protein_coding | deleterious(0.02) | possibly_damaging(0.623) | TCGA-60-2715-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | docetaxel | PD | |
LARP1 | SNV | Missense_Mutation | c.220N>A | p.Ala74Thr | p.A74T | Q6PKG0 | protein_coding | tolerated(0.47) | benign(0.085) | TCGA-85-6560-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD | |
LARP1 | SNV | Missense_Mutation | novel | c.595N>T | p.Pro199Ser | p.P199S | Q6PKG0 | protein_coding | tolerated(0.73) | benign(0.033) | TCGA-CV-A468-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LARP1 | SNV | Missense_Mutation | rs769646240 | c.596N>T | p.Pro199Leu | p.P199L | Q6PKG0 | protein_coding | tolerated(0.28) | benign(0.051) | TCGA-CV-A468-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LARP1 | SNV | Missense_Mutation | novel | c.555N>C | p.Glu185Asp | p.E185D | Q6PKG0 | protein_coding | tolerated(0.49) | benign(0.006) | TCGA-XJ-A83F-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 7 | Unknown | Unknown | SD |
LARP1 | SNV | Missense_Mutation | rs755236202 | c.1115N>T | p.Ala372Val | p.A372V | Q6PKG0 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
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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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