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Gene: LMBRD1 |
Gene summary for LMBRD1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LMBRD1 | Gene ID | 55788 |
Gene name | LMBR1 domain containing 1 | |
Gene Alias | C6orf209 | |
Cytomap | 6q13 | |
Gene Type | protein-coding | GO ID | GO:0006725 | UniProtAcc | Q9NUN5 |
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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 |
55788 | LMBRD1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.26e-08 | -4.68e-01 | 0.0155 |
55788 | LMBRD1 | HTA11_696_2000001011 | Human | Colorectum | AD | 8.19e-06 | -3.41e-01 | -0.1464 |
55788 | LMBRD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.15e-03 | -3.75e-01 | 0.096 |
55788 | LMBRD1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.52e-05 | -3.71e-01 | 0.0674 |
55788 | LMBRD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.18e-08 | -3.87e-01 | 0.3005 |
55788 | LMBRD1 | A002-C-010 | Human | Colorectum | FAP | 5.84e-06 | -2.36e-01 | 0.242 |
55788 | LMBRD1 | A001-C-207 | Human | Colorectum | FAP | 3.84e-05 | -3.98e-01 | 0.1278 |
55788 | LMBRD1 | A015-C-203 | Human | Colorectum | FAP | 1.98e-23 | -4.71e-01 | -0.1294 |
55788 | LMBRD1 | A015-C-204 | Human | Colorectum | FAP | 3.51e-06 | -4.04e-01 | -0.0228 |
55788 | LMBRD1 | A014-C-040 | Human | Colorectum | FAP | 7.46e-03 | -4.29e-01 | -0.1184 |
55788 | LMBRD1 | A002-C-201 | Human | Colorectum | FAP | 2.18e-10 | -3.91e-01 | 0.0324 |
55788 | LMBRD1 | A002-C-203 | Human | Colorectum | FAP | 3.39e-04 | -2.14e-01 | 0.2786 |
55788 | LMBRD1 | A001-C-119 | Human | Colorectum | FAP | 1.18e-11 | -5.46e-01 | -0.1557 |
55788 | LMBRD1 | A001-C-108 | Human | Colorectum | FAP | 5.01e-20 | -4.17e-01 | -0.0272 |
55788 | LMBRD1 | A002-C-205 | Human | Colorectum | FAP | 5.09e-17 | -4.93e-01 | -0.1236 |
55788 | LMBRD1 | A001-C-104 | Human | Colorectum | FAP | 1.81e-09 | -3.98e-01 | 0.0184 |
55788 | LMBRD1 | A015-C-005 | Human | Colorectum | FAP | 8.81e-07 | -3.63e-01 | -0.0336 |
55788 | LMBRD1 | A015-C-006 | Human | Colorectum | FAP | 5.65e-12 | -5.00e-01 | -0.0994 |
55788 | LMBRD1 | A015-C-106 | Human | Colorectum | FAP | 5.41e-13 | -3.61e-01 | -0.0511 |
55788 | LMBRD1 | A002-C-114 | Human | Colorectum | FAP | 9.39e-15 | -4.77e-01 | -0.1561 |
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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:007266518 | Thyroid | PTC | protein localization to vacuole | 38/5968 | 67/18723 | 2.28e-05 | 2.28e-04 | 38 |
GO:004311219 | Thyroid | PTC | receptor metabolic process | 77/5968 | 166/18723 | 6.21e-05 | 5.47e-04 | 77 |
GO:000736910 | Thyroid | PTC | gastrulation | 84/5968 | 185/18723 | 7.58e-05 | 6.52e-04 | 84 |
GO:006146213 | Thyroid | PTC | protein localization to lysosome | 23/5968 | 46/18723 | 7.89e-03 | 3.33e-02 | 23 |
GO:000689826 | Thyroid | ATC | receptor-mediated endocytosis | 118/6293 | 244/18723 | 1.17e-06 | 1.50e-05 | 118 |
GO:000736915 | Thyroid | ATC | gastrulation | 90/6293 | 185/18723 | 1.54e-05 | 1.43e-04 | 90 |
GO:004311224 | Thyroid | ATC | receptor metabolic process | 82/6293 | 166/18723 | 1.78e-05 | 1.63e-04 | 82 |
GO:007258315 | Thyroid | ATC | clathrin-dependent endocytosis | 30/6293 | 47/18723 | 2.16e-05 | 1.92e-04 | 30 |
GO:007266523 | Thyroid | ATC | protein localization to vacuole | 38/6293 | 67/18723 | 8.48e-05 | 6.33e-04 | 38 |
GO:003162310 | Thyroid | ATC | receptor internalization | 52/6293 | 113/18723 | 4.05e-03 | 1.74e-02 | 52 |
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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 |
LMBRD1 | SNV | Missense_Mutation | c.1300N>A | p.Gln434Lys | p.Q434K | Q9NUN5 | protein_coding | deleterious(0.01) | possibly_damaging(0.8) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
LMBRD1 | SNV | Missense_Mutation | c.686N>A | p.Ser229Asn | p.S229N | Q9NUN5 | protein_coding | tolerated(0.21) | benign(0.005) | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
LMBRD1 | SNV | Missense_Mutation | c.160C>G | p.Leu54Val | p.L54V | Q9NUN5 | protein_coding | deleterious(0.01) | possibly_damaging(0.832) | TCGA-BH-A0H5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR | |
LMBRD1 | SNV | Missense_Mutation | c.370N>A | p.Glu124Lys | p.E124K | Q9NUN5 | protein_coding | deleterious(0) | benign(0.276) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
LMBRD1 | SNV | Missense_Mutation | c.1382N>T | p.Ser461Phe | p.S461F | Q9NUN5 | protein_coding | tolerated(0.7) | benign(0) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
LMBRD1 | SNV | Missense_Mutation | c.177C>G | p.Ile59Met | p.I59M | Q9NUN5 | protein_coding | tolerated(0.23) | benign(0.159) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
LMBRD1 | SNV | Missense_Mutation | c.379N>T | p.Asp127Tyr | p.D127Y | Q9NUN5 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-JW-A5VI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | topotecan | PD | |
LMBRD1 | insertion | Frame_Shift_Ins | novel | c.1236dupT | p.Leu413SerfsTer13 | p.L413Sfs*13 | Q9NUN5 | protein_coding | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
LMBRD1 | SNV | Missense_Mutation | c.1264N>A | p.Leu422Ile | p.L422I | Q9NUN5 | protein_coding | tolerated(0.12) | possibly_damaging(0.817) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
LMBRD1 | SNV | Missense_Mutation | c.143N>C | p.Ile48Thr | p.I48T | Q9NUN5 | protein_coding | tolerated(0.07) | benign(0.048) | TCGA-AA-3821-01 | Colorectum | colon 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 |
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