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Gene: NCBP1 |
Gene summary for NCBP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NCBP1 | Gene ID | 4686 |
| Gene name | nuclear cap binding protein subunit 1 | |
| Gene Alias | CBP80 | |
| Cytomap | 9q22.33 | |
| Gene Type | protein-coding | GO ID | GO:0000184 | UniProtAcc | A0A024R179 |
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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 |
| 4686 | NCBP1 | LZE4T | Human | Esophagus | ESCC | 1.16e-08 | 2.08e-01 | 0.0811 |
| 4686 | NCBP1 | LZE7T | Human | Esophagus | ESCC | 7.83e-07 | 2.23e-01 | 0.0667 |
| 4686 | NCBP1 | LZE24T | Human | Esophagus | ESCC | 3.30e-11 | 2.92e-01 | 0.0596 |
| 4686 | NCBP1 | LZE6T | Human | Esophagus | ESCC | 2.15e-03 | 1.12e-01 | 0.0845 |
| 4686 | NCBP1 | P1T-E | Human | Esophagus | ESCC | 1.82e-06 | 2.52e-01 | 0.0875 |
| 4686 | NCBP1 | P2T-E | Human | Esophagus | ESCC | 7.44e-16 | 3.48e-01 | 0.1177 |
| 4686 | NCBP1 | P4T-E | Human | Esophagus | ESCC | 1.64e-09 | 2.29e-01 | 0.1323 |
| 4686 | NCBP1 | P5T-E | Human | Esophagus | ESCC | 2.91e-05 | 5.30e-02 | 0.1327 |
| 4686 | NCBP1 | P8T-E | Human | Esophagus | ESCC | 4.11e-03 | 8.02e-02 | 0.0889 |
| 4686 | NCBP1 | P9T-E | Human | Esophagus | ESCC | 6.31e-15 | 1.65e-01 | 0.1131 |
| 4686 | NCBP1 | P10T-E | Human | Esophagus | ESCC | 4.70e-17 | 3.00e-01 | 0.116 |
| 4686 | NCBP1 | P11T-E | Human | Esophagus | ESCC | 5.83e-11 | 2.08e-01 | 0.1426 |
| 4686 | NCBP1 | P12T-E | Human | Esophagus | ESCC | 1.54e-11 | 2.37e-01 | 0.1122 |
| 4686 | NCBP1 | P15T-E | Human | Esophagus | ESCC | 2.87e-19 | 2.87e-01 | 0.1149 |
| 4686 | NCBP1 | P16T-E | Human | Esophagus | ESCC | 1.01e-10 | 1.72e-01 | 0.1153 |
| 4686 | NCBP1 | P17T-E | Human | Esophagus | ESCC | 6.36e-03 | 9.70e-02 | 0.1278 |
| 4686 | NCBP1 | P19T-E | Human | Esophagus | ESCC | 3.22e-05 | 5.02e-01 | 0.1662 |
| 4686 | NCBP1 | P20T-E | Human | Esophagus | ESCC | 1.10e-15 | 1.88e-01 | 0.1124 |
| 4686 | NCBP1 | P21T-E | Human | Esophagus | ESCC | 4.61e-15 | 3.34e-01 | 0.1617 |
| 4686 | NCBP1 | P22T-E | Human | Esophagus | ESCC | 3.33e-12 | 1.70e-01 | 0.1236 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
| GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0006913110 | Esophagus | ESCC | nucleocytoplasmic transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0051169110 | Esophagus | ESCC | nuclear transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0006403110 | Esophagus | ESCC | RNA localization | 166/8552 | 201/18723 | 1.95e-27 | 6.18e-25 | 166 |
| GO:1903311110 | Esophagus | ESCC | regulation of mRNA metabolic process | 210/8552 | 288/18723 | 3.25e-21 | 5.56e-19 | 210 |
| GO:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:005123617 | Esophagus | ESCC | establishment of RNA localization | 134/8552 | 166/18723 | 1.23e-20 | 1.81e-18 | 134 |
| GO:0051168110 | Esophagus | ESCC | nuclear export | 126/8552 | 154/18723 | 1.88e-20 | 2.65e-18 | 126 |
| GO:005102815 | Esophagus | ESCC | mRNA transport | 110/8552 | 130/18723 | 2.76e-20 | 3.80e-18 | 110 |
| GO:0051098111 | Esophagus | ESCC | regulation of binding | 251/8552 | 363/18723 | 6.73e-20 | 8.46e-18 | 251 |
| GO:005065717 | Esophagus | ESCC | nucleic acid transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:005065817 | Esophagus | ESCC | RNA transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:0006413110 | Esophagus | ESCC | translational initiation | 100/8552 | 118/18723 | 1.16e-18 | 1.25e-16 | 100 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0501422 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa03013 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
| hsa0301521 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
| hsa0304022 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0501432 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa030131 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
| hsa0301531 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
| hsa0304032 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0501428 | Oral cavity | OSCC | Amyotrophic lateral sclerosis | 246/3704 | 364/8465 | 6.65e-21 | 1.11e-18 | 5.67e-19 | 246 |
| hsa030136 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
| hsa030158 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
| hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| Page: 1 2 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| NCBP1 | SNV | Missense_Mutation | c.1357C>G | p.Leu453Val | p.L453V | Q09161 | protein_coding | deleterious(0.01) | possibly_damaging(0.877) | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | |
| NCBP1 | SNV | Missense_Mutation | novel | c.397N>A | p.Asp133Asn | p.D133N | Q09161 | protein_coding | deleterious(0.05) | possibly_damaging(0.893) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
| NCBP1 | SNV | Missense_Mutation | novel | c.1325A>G | p.Glu442Gly | p.E442G | Q09161 | protein_coding | tolerated(0.48) | benign(0.005) | TCGA-D8-A27W-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicine+cyclophosphamide | SD |
| NCBP1 | SNV | Missense_Mutation | rs189780807 | c.1829N>A | p.Arg610His | p.R610H | Q09161 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NCBP1 | SNV | Missense_Mutation | novel | c.590N>T | p.Ala197Val | p.A197V | Q09161 | protein_coding | tolerated(0.32) | benign(0.003) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NCBP1 | SNV | Missense_Mutation | novel | c.1215N>A | p.Met405Ile | p.M405I | Q09161 | protein_coding | deleterious(0) | possibly_damaging(0.893) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NCBP1 | SNV | Missense_Mutation | c.1324N>A | p.Glu442Lys | p.E442K | Q09161 | protein_coding | tolerated(0.62) | benign(0.102) | TCGA-Q1-A5R2-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PR | |
| NCBP1 | SNV | Missense_Mutation | c.115N>A | p.Gly39Arg | p.G39R | Q09161 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3695-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| NCBP1 | SNV | Missense_Mutation | c.708N>G | p.Ile236Met | p.I236M | Q09161 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| NCBP1 | SNV | Missense_Mutation | c.1223N>T | p.Thr408Ile | p.T408I | Q09161 | protein_coding | tolerated(0.26) | benign(0.007) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| Page: 1 |
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