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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 |
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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: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 |
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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 |
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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 |
NCBP1 | SNV | Missense_Mutation | c.701N>T | p.Ala234Val | p.A234V | Q09161 | protein_coding | deleterious(0.03) | benign(0.371) | TCGA-AG-A02N-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | folinic | CR | |
NCBP1 | SNV | Missense_Mutation | novel | c.1408N>T | p.Pro470Ser | p.P470S | Q09161 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-EI-6507-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NCBP1 | SNV | Missense_Mutation | c.604T>A | p.Tyr202Asn | p.Y202N | Q09161 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-EI-6881-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5 | SD | |
NCBP1 | SNV | Missense_Mutation | c.1548N>C | p.Glu516Asp | p.E516D | Q09161 | protein_coding | tolerated(0.12) | benign(0.159) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
NCBP1 | insertion | Frame_Shift_Ins | novel | c.2121_2122insGAAAATACCATTT | p.Asn708GlufsTer5 | p.N708Efs*5 | Q09161 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
NCBP1 | SNV | Missense_Mutation | novel | c.185N>A | p.Pro62His | p.P62H | Q09161 | protein_coding | deleterious(0.04) | benign(0.316) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NCBP1 | SNV | Missense_Mutation | novel | c.1154N>A | p.Gly385Asp | p.G385D | Q09161 | protein_coding | tolerated(0.2) | benign(0.03) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NCBP1 | SNV | Missense_Mutation | c.2367N>T | p.Gln789His | p.Q789H | Q09161 | protein_coding | tolerated(0.06) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
NCBP1 | SNV | Missense_Mutation | c.860T>C | p.Val287Ala | p.V287A | Q09161 | protein_coding | deleterious(0) | probably_damaging(0.936) | TCGA-A5-A0GP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
NCBP1 | SNV | Missense_Mutation | c.1228N>A | p.Val410Ile | p.V410I | Q09161 | protein_coding | tolerated(1) | benign(0.006) | TCGA-A5-A0VP-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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