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Gene: NLRC5 |
Gene summary for NLRC5 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NLRC5 | Gene ID | 84166 |
Gene name | NLR family CARD domain containing 5 | |
Gene Alias | CLR16.1 | |
Cytomap | 16q13 | |
Gene Type | protein-coding | GO ID | GO:0001959 | UniProtAcc | Q86WI3 |
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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 |
84166 | NLRC5 | CCI_1 | Human | Cervix | CC | 7.61e-06 | 5.43e-01 | 0.528 |
84166 | NLRC5 | CCI_2 | Human | Cervix | CC | 5.06e-18 | 1.22e+00 | 0.5249 |
84166 | NLRC5 | CCI_3 | Human | Cervix | CC | 1.61e-14 | 7.68e-01 | 0.516 |
84166 | NLRC5 | sample3 | Human | Cervix | CC | 4.31e-06 | 1.64e-01 | 0.1387 |
84166 | NLRC5 | T1 | Human | Cervix | CC | 8.93e-05 | 3.19e-01 | 0.0918 |
84166 | NLRC5 | HTA11_347_2000001011 | Human | Colorectum | AD | 8.49e-08 | 3.20e-01 | -0.1954 |
84166 | NLRC5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.96e-11 | 6.70e-01 | -0.059 |
84166 | NLRC5 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.31e-03 | 8.85e-01 | 0.3487 |
84166 | NLRC5 | A002-C-010 | Human | Colorectum | FAP | 8.52e-03 | -1.41e-01 | 0.242 |
84166 | NLRC5 | A015-C-203 | Human | Colorectum | FAP | 5.18e-10 | -2.09e-01 | -0.1294 |
84166 | NLRC5 | A002-C-203 | Human | Colorectum | FAP | 7.55e-04 | -2.29e-01 | 0.2786 |
84166 | NLRC5 | A001-C-108 | Human | Colorectum | FAP | 3.34e-08 | -2.31e-01 | -0.0272 |
84166 | NLRC5 | A001-C-104 | Human | Colorectum | FAP | 1.27e-03 | -2.29e-01 | 0.0184 |
84166 | NLRC5 | A015-C-106 | Human | Colorectum | FAP | 1.09e-02 | -1.31e-02 | -0.0511 |
84166 | NLRC5 | A015-C-104 | Human | Colorectum | FAP | 3.11e-09 | -1.91e-01 | -0.1899 |
84166 | NLRC5 | A001-C-014 | Human | Colorectum | FAP | 1.34e-07 | -2.22e-01 | 0.0135 |
84166 | NLRC5 | A002-C-016 | Human | Colorectum | FAP | 2.29e-06 | -1.70e-01 | 0.0521 |
84166 | NLRC5 | A001-C-203 | Human | Colorectum | FAP | 5.53e-03 | -1.76e-01 | -0.0481 |
84166 | NLRC5 | A002-C-116 | Human | Colorectum | FAP | 2.30e-08 | -1.12e-01 | -0.0452 |
84166 | NLRC5 | A018-E-020 | Human | Colorectum | FAP | 2.51e-02 | -2.43e-01 | -0.2034 |
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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:00321035 | Cervix | CC | positive regulation of response to external stimulus | 95/2311 | 427/18723 | 5.44e-09 | 5.03e-07 | 95 |
GO:00026837 | Cervix | CC | negative regulation of immune system process | 94/2311 | 434/18723 | 2.63e-08 | 1.87e-06 | 94 |
GO:00510904 | Cervix | CC | regulation of DNA-binding transcription factor activity | 87/2311 | 440/18723 | 4.85e-06 | 1.22e-04 | 87 |
GO:00313494 | Cervix | CC | positive regulation of defense response | 60/2311 | 278/18723 | 9.38e-06 | 2.11e-04 | 60 |
GO:00028315 | Cervix | CC | regulation of response to biotic stimulus | 67/2311 | 327/18723 | 1.79e-05 | 3.36e-04 | 67 |
GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
GO:00028322 | Cervix | CC | negative regulation of response to biotic stimulus | 27/2311 | 108/18723 | 2.27e-04 | 2.55e-03 | 27 |
GO:00192213 | Cervix | CC | cytokine-mediated signaling pathway | 84/2311 | 472/18723 | 3.25e-04 | 3.44e-03 | 84 |
GO:00507773 | Cervix | CC | negative regulation of immune response | 41/2311 | 194/18723 | 3.63e-04 | 3.76e-03 | 41 |
GO:00321022 | Cervix | CC | negative regulation of response to external stimulus | 75/2311 | 420/18723 | 5.96e-04 | 5.61e-03 | 75 |
GO:00450882 | Cervix | CC | regulation of innate immune response | 44/2311 | 218/18723 | 6.40e-04 | 5.97e-03 | 44 |
GO:00028331 | Cervix | CC | positive regulation of response to biotic stimulus | 35/2311 | 168/18723 | 1.23e-03 | 9.87e-03 | 35 |
GO:00343415 | Cervix | CC | response to interferon-gamma | 30/2311 | 141/18723 | 1.88e-03 | 1.39e-02 | 30 |
GO:00458243 | Cervix | CC | negative regulation of innate immune response | 18/2311 | 71/18723 | 2.01e-03 | 1.47e-02 | 18 |
GO:0031348 | Cervix | CC | negative regulation of defense response | 48/2311 | 258/18723 | 2.30e-03 | 1.65e-02 | 48 |
GO:00603333 | Cervix | CC | interferon-gamma-mediated signaling pathway | 9/2311 | 27/18723 | 3.82e-03 | 2.41e-02 | 9 |
GO:00713463 | Cervix | CC | cellular response to interferon-gamma | 25/2311 | 118/18723 | 4.54e-03 | 2.75e-02 | 25 |
GO:00019612 | Cervix | CC | positive regulation of cytokine-mediated signaling pathway | 13/2311 | 50/18723 | 6.42e-03 | 3.58e-02 | 13 |
GO:00607602 | Cervix | CC | positive regulation of response to cytokine stimulus | 14/2311 | 57/18723 | 8.17e-03 | 4.25e-02 | 14 |
GO:0045089 | Cervix | CC | positive regulation of innate immune response | 26/2311 | 131/18723 | 9.33e-03 | 4.66e-02 | 26 |
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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 |
NLRC5 | SNV | Missense_Mutation | c.593N>G | p.Asp198Gly | p.D198G | Q86WI3 | protein_coding | tolerated(0.32) | benign(0.003) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
NLRC5 | SNV | Missense_Mutation | rs201268786 | c.364N>T | p.Arg122Cys | p.R122C | Q86WI3 | protein_coding | deleterious(0) | probably_damaging(0.925) | TCGA-D7-A4YY-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
NLRC5 | SNV | Missense_Mutation | novel | c.4720C>A | p.Leu1574Ile | p.L1574I | Q86WI3 | protein_coding | deleterious(0.04) | probably_damaging(0.929) | TCGA-D7-A6EX-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
NLRC5 | SNV | Missense_Mutation | novel | c.1571N>C | p.Leu524Pro | p.L524P | Q86WI3 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-HF-A5NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | SD |
NLRC5 | SNV | Missense_Mutation | novel | c.980T>C | p.Leu327Pro | p.L327P | Q86WI3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-R5-A7ZI-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NLRC5 | SNV | Missense_Mutation | novel | c.5548N>G | p.Arg1850Gly | p.R1850G | Q86WI3 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-VQ-A8PO-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
NLRC5 | deletion | Frame_Shift_Del | novel | c.5231_5234delNNNN | p.Ile1745ThrfsTer27 | p.I1745Tfs*27 | Q86WI3 | protein_coding | TCGA-BR-7703-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
NLRC5 | deletion | Frame_Shift_Del | novel | c.5231_5234delNNNN | p.Ile1745ThrfsTer27 | p.I1745Tfs*27 | Q86WI3 | protein_coding | TCGA-BR-7851-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
NLRC5 | insertion | Frame_Shift_Ins | novel | c.3375_3376insT | p.Arg1126SerfsTer20 | p.R1126Sfs*20 | Q86WI3 | protein_coding | TCGA-BR-A4CS-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
NLRC5 | deletion | Frame_Shift_Del | novel | c.3580delN | p.Lys1195ArgfsTer38 | p.K1195Rfs*38 | Q86WI3 | protein_coding | TCGA-F1-A448-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR |
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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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