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Gene: NHLRC3 |
Gene summary for NHLRC3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NHLRC3 | Gene ID | 387921 |
Gene name | NHL repeat containing 3 | |
Gene Alias | NHLRC3 | |
Cytomap | 13q13.3 | |
Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | Q5JS37 |
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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 |
387921 | NHLRC3 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.75e-02 | 2.87e-01 | -0.1954 |
387921 | NHLRC3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.74e-05 | 6.43e-01 | 0.281 |
387921 | NHLRC3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.04e-09 | 6.40e-01 | 0.3859 |
387921 | NHLRC3 | A015-C-203 | Human | Colorectum | FAP | 6.03e-07 | -2.15e-01 | -0.1294 |
387921 | NHLRC3 | A015-C-204 | Human | Colorectum | FAP | 4.92e-03 | -2.11e-01 | -0.0228 |
387921 | NHLRC3 | A002-C-201 | Human | Colorectum | FAP | 2.74e-04 | -1.75e-01 | 0.0324 |
387921 | NHLRC3 | A001-C-108 | Human | Colorectum | FAP | 2.75e-05 | -1.74e-01 | -0.0272 |
387921 | NHLRC3 | A002-C-205 | Human | Colorectum | FAP | 3.93e-06 | -1.79e-01 | -0.1236 |
387921 | NHLRC3 | A015-C-006 | Human | Colorectum | FAP | 1.05e-04 | -1.88e-01 | -0.0994 |
387921 | NHLRC3 | A015-C-106 | Human | Colorectum | FAP | 3.16e-02 | -1.13e-01 | -0.0511 |
387921 | NHLRC3 | A002-C-114 | Human | Colorectum | FAP | 3.60e-06 | -2.39e-01 | -0.1561 |
387921 | NHLRC3 | A015-C-104 | Human | Colorectum | FAP | 3.02e-08 | -2.07e-01 | -0.1899 |
387921 | NHLRC3 | A001-C-014 | Human | Colorectum | FAP | 4.03e-03 | -1.69e-01 | 0.0135 |
387921 | NHLRC3 | A002-C-016 | Human | Colorectum | FAP | 1.97e-06 | -1.62e-01 | 0.0521 |
387921 | NHLRC3 | A015-C-002 | Human | Colorectum | FAP | 2.10e-02 | -1.14e-01 | -0.0763 |
387921 | NHLRC3 | A002-C-116 | Human | Colorectum | FAP | 4.08e-10 | -2.27e-01 | -0.0452 |
387921 | NHLRC3 | A014-C-008 | Human | Colorectum | FAP | 3.20e-03 | -1.65e-01 | -0.191 |
387921 | NHLRC3 | A018-E-020 | Human | Colorectum | FAP | 2.30e-05 | -1.71e-01 | -0.2034 |
387921 | NHLRC3 | F034 | Human | Colorectum | FAP | 2.11e-05 | -1.69e-01 | -0.0665 |
387921 | NHLRC3 | CRC-1-8810 | Human | Colorectum | CRC | 2.21e-05 | 3.96e-01 | 0.6257 |
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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:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
GO:0000209 | Colorectum | AD | protein polyubiquitination | 78/3918 | 236/18723 | 8.71e-06 | 2.06e-04 | 78 |
GO:00104982 | Colorectum | MSS | proteasomal protein catabolic process | 157/3467 | 490/18723 | 2.39e-13 | 5.25e-11 | 157 |
GO:00431612 | Colorectum | MSS | proteasome-mediated ubiquitin-dependent protein catabolic process | 127/3467 | 412/18723 | 7.70e-10 | 6.32e-08 | 127 |
GO:00002092 | Colorectum | MSS | protein polyubiquitination | 72/3467 | 236/18723 | 5.19e-06 | 1.42e-04 | 72 |
GO:00431614 | Colorectum | FAP | proteasome-mediated ubiquitin-dependent protein catabolic process | 98/2622 | 412/18723 | 5.41e-08 | 4.20e-06 | 98 |
GO:00104984 | Colorectum | FAP | proteasomal protein catabolic process | 110/2622 | 490/18723 | 2.12e-07 | 1.26e-05 | 110 |
GO:00002093 | Colorectum | FAP | protein polyubiquitination | 59/2622 | 236/18723 | 4.53e-06 | 1.52e-04 | 59 |
GO:00002094 | Colorectum | CRC | protein polyubiquitination | 46/2078 | 236/18723 | 9.91e-05 | 1.98e-03 | 46 |
GO:00431615 | Colorectum | CRC | proteasome-mediated ubiquitin-dependent protein catabolic process | 69/2078 | 412/18723 | 3.16e-04 | 4.90e-03 | 69 |
GO:00104985 | Colorectum | CRC | proteasomal protein catabolic process | 77/2078 | 490/18723 | 1.03e-03 | 1.21e-02 | 77 |
GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
GO:004316120 | Oral cavity | OSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 285/7305 | 412/18723 | 5.68e-36 | 5.99e-33 | 285 |
GO:000020910 | Oral cavity | OSCC | protein polyubiquitination | 150/7305 | 236/18723 | 1.59e-14 | 9.27e-13 | 150 |
GO:0010498110 | Oral cavity | LP | proteasomal protein catabolic process | 224/4623 | 490/18723 | 9.57e-25 | 4.00e-22 | 224 |
GO:0043161110 | Oral cavity | LP | proteasome-mediated ubiquitin-dependent protein catabolic process | 190/4623 | 412/18723 | 1.08e-21 | 2.93e-19 | 190 |
GO:000020915 | Oral cavity | LP | protein polyubiquitination | 82/4623 | 236/18723 | 3.23e-04 | 3.26e-03 | 82 |
GO:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
GO:0043161113 | Thyroid | PTC | proteasome-mediated ubiquitin-dependent protein catabolic process | 254/5968 | 412/18723 | 3.91e-36 | 4.54e-33 | 254 |
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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 |
NHLRC3 | SNV | Missense_Mutation | c.390N>A | p.Phe130Leu | p.F130L | Q5JS37 | protein_coding | tolerated(0.28) | benign(0.001) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NHLRC3 | SNV | Missense_Mutation | c.82N>T | p.Pro28Ser | p.P28S | Q5JS37 | protein_coding | tolerated_low_confidence(0.24) | benign(0.003) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
NHLRC3 | SNV | Missense_Mutation | c.741N>T | p.Trp247Cys | p.W247C | Q5JS37 | protein_coding | deleterious(0) | possibly_damaging(0.635) | TCGA-CK-5914-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
NHLRC3 | SNV | Missense_Mutation | c.121A>G | p.Thr41Ala | p.T41A | Q5JS37 | protein_coding | tolerated_low_confidence(0.73) | benign(0) | TCGA-DY-A1DC-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Chemotherapy | capecitabine | PR | |
NHLRC3 | SNV | Missense_Mutation | novel | c.629N>A | p.Pro210His | p.P210H | Q5JS37 | protein_coding | tolerated(0.08) | possibly_damaging(0.864) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NHLRC3 | SNV | Missense_Mutation | novel | c.278A>G | p.Asp93Gly | p.D93G | Q5JS37 | protein_coding | deleterious(0.01) | possibly_damaging(0.704) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NHLRC3 | SNV | Missense_Mutation | novel | c.380G>T | p.Gly127Val | p.G127V | Q5JS37 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NHLRC3 | SNV | Missense_Mutation | c.193T>G | p.Cys65Gly | p.C65G | Q5JS37 | protein_coding | tolerated(0.25) | benign(0) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
NHLRC3 | SNV | Missense_Mutation | c.707N>T | p.Arg236Ile | p.R236I | Q5JS37 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
NHLRC3 | SNV | Missense_Mutation | novel | c.401N>T | p.Thr134Ile | p.T134I | Q5JS37 | protein_coding | deleterious(0.01) | possibly_damaging(0.654) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | 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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