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Gene: NPLOC4 |
Gene summary for NPLOC4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NPLOC4 | Gene ID | 55666 |
Gene name | NPL4 homolog, ubiquitin recognition factor | |
Gene Alias | NPL4 | |
Cytomap | 17q25.3 | |
Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | A0A024R8R4 |
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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 |
55666 | NPLOC4 | CCI_1 | Human | Cervix | CC | 3.24e-04 | 6.65e-01 | 0.528 |
55666 | NPLOC4 | CCI_3 | Human | Cervix | CC | 1.47e-12 | 8.32e-01 | 0.516 |
55666 | NPLOC4 | sample3 | Human | Cervix | CC | 2.62e-04 | 2.04e-01 | 0.1387 |
55666 | NPLOC4 | T3 | Human | Cervix | CC | 4.09e-07 | 2.27e-01 | 0.1389 |
55666 | NPLOC4 | AEH-subject1 | Human | Endometrium | AEH | 2.68e-06 | 2.50e-01 | -0.3059 |
55666 | NPLOC4 | AEH-subject4 | Human | Endometrium | AEH | 1.39e-04 | 2.58e-01 | -0.2657 |
55666 | NPLOC4 | EEC-subject1 | Human | Endometrium | EEC | 1.66e-03 | 2.37e-01 | -0.2682 |
55666 | NPLOC4 | EEC-subject3 | Human | Endometrium | EEC | 4.18e-02 | 8.91e-02 | -0.2525 |
55666 | NPLOC4 | EEC-subject5 | Human | Endometrium | EEC | 4.00e-09 | 3.46e-01 | -0.249 |
55666 | NPLOC4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 6.41e-03 | -1.24e-04 | -0.1869 |
55666 | NPLOC4 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 7.31e-05 | 1.34e-02 | -0.1934 |
55666 | NPLOC4 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 4.95e-07 | -2.07e-03 | -0.1917 |
55666 | NPLOC4 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 6.59e-05 | -3.77e-02 | -0.1916 |
55666 | NPLOC4 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 3.50e-09 | 3.80e-01 | -0.1269 |
55666 | NPLOC4 | LZE2T | Human | Esophagus | ESCC | 1.86e-02 | 4.33e-01 | 0.082 |
55666 | NPLOC4 | LZE7T | Human | Esophagus | ESCC | 2.05e-08 | 4.39e-01 | 0.0667 |
55666 | NPLOC4 | LZE20T | Human | Esophagus | ESCC | 1.25e-02 | 1.05e-01 | 0.0662 |
55666 | NPLOC4 | LZE22T | Human | Esophagus | ESCC | 3.08e-06 | 3.07e-01 | 0.068 |
55666 | NPLOC4 | LZE24T | Human | Esophagus | ESCC | 2.49e-08 | 2.61e-01 | 0.0596 |
55666 | NPLOC4 | LZE21T | Human | Esophagus | ESCC | 2.40e-02 | 1.72e-01 | 0.0655 |
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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:001049810 | Cervix | CC | proteasomal protein catabolic process | 111/2311 | 490/18723 | 8.98e-11 | 1.58e-08 | 111 |
GO:004316110 | Cervix | CC | proteasome-mediated ubiquitin-dependent protein catabolic process | 91/2311 | 412/18723 | 1.65e-08 | 1.25e-06 | 91 |
GO:00026837 | Cervix | CC | negative regulation of immune system process | 94/2311 | 434/18723 | 2.63e-08 | 1.87e-06 | 94 |
GO:00027644 | Cervix | CC | immune response-regulating signaling pathway | 97/2311 | 468/18723 | 1.49e-07 | 7.07e-06 | 97 |
GO:00305229 | Cervix | CC | intracellular receptor signaling pathway | 60/2311 | 265/18723 | 1.89e-06 | 5.97e-05 | 60 |
GO:003497610 | Cervix | CC | response to endoplasmic reticulum stress | 57/2311 | 256/18723 | 5.81e-06 | 1.42e-04 | 57 |
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:00022212 | Cervix | CC | pattern recognition receptor signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
GO:00622073 | Cervix | CC | regulation of pattern recognition receptor signaling pathway | 27/2311 | 105/18723 | 1.37e-04 | 1.68e-03 | 27 |
GO:00027534 | Cervix | CC | cytoplasmic pattern recognition receptor signaling pathway | 18/2311 | 60/18723 | 2.26e-04 | 2.55e-03 | 18 |
GO:00028322 | Cervix | CC | negative regulation of response to biotic stimulus | 27/2311 | 108/18723 | 2.27e-04 | 2.55e-03 | 27 |
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:00395292 | Cervix | CC | RIG-I signaling pathway | 10/2311 | 27/18723 | 9.25e-04 | 7.84e-03 | 10 |
GO:00395352 | Cervix | CC | regulation of RIG-I signaling pathway | 8/2311 | 20/18723 | 1.69e-03 | 1.29e-02 | 8 |
GO:0031348 | Cervix | CC | negative regulation of defense response | 48/2311 | 258/18723 | 2.30e-03 | 1.65e-02 | 48 |
GO:00985863 | Cervix | CC | cellular response to virus | 20/2311 | 84/18723 | 2.62e-03 | 1.81e-02 | 20 |
GO:00070304 | Cervix | CC | Golgi organization | 32/2311 | 157/18723 | 2.78e-03 | 1.87e-02 | 32 |
GO:00324791 | Cervix | CC | regulation of type I interferon production | 21/2311 | 95/18723 | 5.32e-03 | 3.10e-02 | 21 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0414120 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
hsa04141110 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
hsa0414126 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
hsa04141111 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
hsa0414127 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
hsa0414136 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
hsa04141211 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
hsa04141310 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
hsa0414114 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa0414115 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa0414122 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0414132 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0414116 | Lung | IAC | Protein processing in endoplasmic reticulum | 37/1053 | 174/8465 | 6.53e-04 | 5.73e-03 | 3.81e-03 | 37 |
hsa0414117 | Lung | IAC | Protein processing in endoplasmic reticulum | 37/1053 | 174/8465 | 6.53e-04 | 5.73e-03 | 3.81e-03 | 37 |
hsa0414123 | Lung | AIS | Protein processing in endoplasmic reticulum | 35/961 | 174/8465 | 4.88e-04 | 4.39e-03 | 2.81e-03 | 35 |
hsa0414133 | Lung | AIS | Protein processing in endoplasmic reticulum | 35/961 | 174/8465 | 4.88e-04 | 4.39e-03 | 2.81e-03 | 35 |
hsa0414130 | Oral cavity | OSCC | Protein processing in endoplasmic reticulum | 143/3704 | 174/8465 | 6.82e-26 | 2.28e-23 | 1.16e-23 | 143 |
hsa04141113 | Oral cavity | OSCC | Protein processing in endoplasmic reticulum | 143/3704 | 174/8465 | 6.82e-26 | 2.28e-23 | 1.16e-23 | 143 |
hsa04141210 | Oral cavity | LP | Protein processing in endoplasmic reticulum | 113/2418 | 174/8465 | 8.74e-24 | 5.82e-22 | 3.76e-22 | 113 |
hsa0414138 | Oral cavity | LP | Protein processing in endoplasmic reticulum | 113/2418 | 174/8465 | 8.74e-24 | 5.82e-22 | 3.76e-22 | 113 |
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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 |
NPLOC4 | SNV | Missense_Mutation | c.161G>A | p.Gly54Glu | p.G54E | Q8TAT6 | protein_coding | tolerated(0.59) | benign(0.079) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
NPLOC4 | SNV | Missense_Mutation | rs763449135 | c.973G>A | p.Val325Ile | p.V325I | Q8TAT6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
NPLOC4 | SNV | Missense_Mutation | novel | c.1409N>A | p.Pro470Gln | p.P470Q | Q8TAT6 | protein_coding | tolerated(0.15) | benign(0.009) | TCGA-AA-A029-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
NPLOC4 | SNV | Missense_Mutation | rs758048463 | c.583N>A | p.Glu195Lys | p.E195K | Q8TAT6 | protein_coding | tolerated(0.91) | benign(0.039) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
NPLOC4 | SNV | Missense_Mutation | c.392N>A | p.Arg131His | p.R131H | Q8TAT6 | protein_coding | tolerated(0.43) | benign(0.015) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NPLOC4 | SNV | Missense_Mutation | c.986N>A | p.Arg329Gln | p.R329Q | Q8TAT6 | protein_coding | deleterious(0.01) | possibly_damaging(0.518) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NPLOC4 | SNV | Missense_Mutation | novel | c.682N>C | p.Phe228Leu | p.F228L | Q8TAT6 | protein_coding | deleterious(0.03) | probably_damaging(0.943) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NPLOC4 | deletion | Frame_Shift_Del | c.747delN | p.Phe249LeufsTer88 | p.F249Lfs*88 | Q8TAT6 | protein_coding | TCGA-F4-6703-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |||
NPLOC4 | SNV | Missense_Mutation | novel | c.602N>T | p.Pro201Leu | p.P201L | Q8TAT6 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NPLOC4 | SNV | Missense_Mutation | novel | c.1400N>T | p.Ser467Leu | p.S467L | Q8TAT6 | protein_coding | tolerated(0.21) | benign(0.131) | TCGA-A5-A2K5-01 | 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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