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Gene: LYRM1 |
Gene summary for LYRM1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LYRM1 | Gene ID | 57149 |
Gene name | LYR motif containing 1 | |
Gene Alias | A211C6.1 | |
Cytomap | 16p12.3 | |
Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | A0A024R3C2 |
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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 |
57149 | LYRM1 | LZE4T | Human | Esophagus | ESCC | 4.86e-12 | 2.46e-01 | 0.0811 |
57149 | LYRM1 | LZE7T | Human | Esophagus | ESCC | 7.33e-05 | 4.54e-01 | 0.0667 |
57149 | LYRM1 | LZE8T | Human | Esophagus | ESCC | 6.16e-05 | 2.44e-01 | 0.067 |
57149 | LYRM1 | LZE20T | Human | Esophagus | ESCC | 1.18e-03 | 1.01e-01 | 0.0662 |
57149 | LYRM1 | LZE24T | Human | Esophagus | ESCC | 3.36e-12 | 3.08e-01 | 0.0596 |
57149 | LYRM1 | LZE21T | Human | Esophagus | ESCC | 9.32e-04 | 2.01e-01 | 0.0655 |
57149 | LYRM1 | LZE6T | Human | Esophagus | ESCC | 3.23e-05 | 1.36e-01 | 0.0845 |
57149 | LYRM1 | P1T-E | Human | Esophagus | ESCC | 3.82e-09 | 2.61e-01 | 0.0875 |
57149 | LYRM1 | P2T-E | Human | Esophagus | ESCC | 5.56e-26 | 5.05e-01 | 0.1177 |
57149 | LYRM1 | P4T-E | Human | Esophagus | ESCC | 2.85e-23 | 4.45e-01 | 0.1323 |
57149 | LYRM1 | P5T-E | Human | Esophagus | ESCC | 1.74e-08 | 1.54e-01 | 0.1327 |
57149 | LYRM1 | P8T-E | Human | Esophagus | ESCC | 6.37e-19 | 3.05e-01 | 0.0889 |
57149 | LYRM1 | P9T-E | Human | Esophagus | ESCC | 1.94e-08 | 2.50e-01 | 0.1131 |
57149 | LYRM1 | P10T-E | Human | Esophagus | ESCC | 5.52e-19 | 3.19e-01 | 0.116 |
57149 | LYRM1 | P11T-E | Human | Esophagus | ESCC | 1.37e-02 | 1.10e-01 | 0.1426 |
57149 | LYRM1 | P12T-E | Human | Esophagus | ESCC | 1.42e-20 | 3.38e-01 | 0.1122 |
57149 | LYRM1 | P15T-E | Human | Esophagus | ESCC | 1.11e-11 | 1.84e-01 | 0.1149 |
57149 | LYRM1 | P16T-E | Human | Esophagus | ESCC | 1.34e-28 | 5.08e-01 | 0.1153 |
57149 | LYRM1 | P17T-E | Human | Esophagus | ESCC | 1.24e-05 | 2.32e-01 | 0.1278 |
57149 | LYRM1 | P19T-E | Human | Esophagus | ESCC | 3.45e-05 | 4.66e-01 | 0.1662 |
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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 |
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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 |
LYRM1 | SNV | Missense_Mutation | novel | c.352N>T | p.His118Tyr | p.H118Y | O43325 | protein_coding | tolerated(0.52) | benign(0) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
LYRM1 | SNV | Missense_Mutation | novel | c.48N>G | p.Ile16Met | p.I16M | O43325 | protein_coding | deleterious(0) | possibly_damaging(0.782) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
LYRM1 | SNV | Missense_Mutation | novel | c.209N>T | p.Arg70Met | p.R70M | O43325 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
LYRM1 | SNV | Missense_Mutation | rs748762247 | c.250N>T | p.Pro84Ser | p.P84S | O43325 | protein_coding | tolerated(0.08) | possibly_damaging(0.878) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
LYRM1 | SNV | Missense_Mutation | c.350N>A | p.Ser117Tyr | p.S117Y | O43325 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
LYRM1 | SNV | Missense_Mutation | novel | c.146N>A | p.Arg49Gln | p.R49Q | O43325 | protein_coding | tolerated(0.51) | benign(0) | TCGA-EC-A24G-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
LYRM1 | SNV | Missense_Mutation | novel | c.221N>T | p.Gly74Val | p.G74V | O43325 | protein_coding | deleterious(0) | possibly_damaging(0.794) | TCGA-22-1011-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LYRM1 | SNV | Missense_Mutation | novel | c.195T>G | p.Asp65Glu | p.D65E | O43325 | protein_coding | tolerated(1) | benign(0) | TCGA-22-1016-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LYRM1 | insertion | In_Frame_Ins | novel | c.90_91insTACAGTTTTTTTTTTTTTTTTTTTTTT | p.Met30_Glu31insTyrSerPhePhePhePhePhePhePhe | p.M30_E31insYSFFFFFFF | O43325 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | 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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