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Gene: TPCN1 |
Gene summary for TPCN1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | TPCN1 | Gene ID | 53373 |
Gene name | two pore segment channel 1 | |
Gene Alias | TPC1 | |
Cytomap | 12q24.13 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | B3KSG7 |
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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 |
53373 | TPCN1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.37e-16 | 6.46e-01 | -0.1954 |
53373 | TPCN1 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.76e-05 | 9.11e-01 | -0.2602 |
53373 | TPCN1 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.84e-04 | 4.90e-01 | -0.1526 |
53373 | TPCN1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.66e-04 | 4.89e-01 | -0.1464 |
53373 | TPCN1 | HTA11_866_2000001011 | Human | Colorectum | AD | 6.52e-05 | 4.04e-01 | -0.1001 |
53373 | TPCN1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.85e-02 | 3.28e-01 | -0.059 |
53373 | TPCN1 | A015-C-203 | Human | Colorectum | FAP | 2.93e-15 | -1.52e-01 | -0.1294 |
53373 | TPCN1 | A002-C-201 | Human | Colorectum | FAP | 1.45e-04 | -3.63e-02 | 0.0324 |
53373 | TPCN1 | A001-C-108 | Human | Colorectum | FAP | 5.16e-05 | -4.05e-02 | -0.0272 |
53373 | TPCN1 | A002-C-205 | Human | Colorectum | FAP | 2.77e-11 | -1.53e-01 | -0.1236 |
53373 | TPCN1 | A015-C-006 | Human | Colorectum | FAP | 3.36e-08 | -6.91e-02 | -0.0994 |
53373 | TPCN1 | A015-C-106 | Human | Colorectum | FAP | 1.44e-03 | -5.86e-02 | -0.0511 |
53373 | TPCN1 | A002-C-114 | Human | Colorectum | FAP | 1.72e-09 | -1.46e-01 | -0.1561 |
53373 | TPCN1 | A015-C-104 | Human | Colorectum | FAP | 4.22e-16 | -8.42e-02 | -0.1899 |
53373 | TPCN1 | A015-C-202 | Human | Colorectum | FAP | 4.58e-04 | 2.93e-01 | -0.0849 |
53373 | TPCN1 | A001-C-014 | Human | Colorectum | FAP | 4.68e-06 | -1.46e-01 | 0.0135 |
53373 | TPCN1 | A002-C-016 | Human | Colorectum | FAP | 4.44e-11 | -2.57e-01 | 0.0521 |
53373 | TPCN1 | A015-C-002 | Human | Colorectum | FAP | 3.35e-05 | -2.25e-01 | -0.0763 |
53373 | TPCN1 | A001-C-203 | Human | Colorectum | FAP | 8.40e-03 | -7.99e-03 | -0.0481 |
53373 | TPCN1 | A002-C-116 | Human | Colorectum | FAP | 6.82e-21 | -2.65e-01 | -0.0452 |
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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:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
GO:0009896 | Colorectum | AD | positive regulation of catabolic process | 180/3918 | 492/18723 | 4.33e-16 | 1.94e-13 | 180 |
GO:0031331 | Colorectum | AD | positive regulation of cellular catabolic process | 156/3918 | 427/18723 | 4.68e-14 | 1.05e-11 | 156 |
GO:0019058 | Colorectum | AD | viral life cycle | 119/3918 | 317/18723 | 6.18e-12 | 8.23e-10 | 119 |
GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
GO:0044403 | Colorectum | AD | biological process involved in symbiotic interaction | 99/3918 | 290/18723 | 1.02e-07 | 4.93e-06 | 99 |
GO:0051701 | Colorectum | AD | biological process involved in interaction with host | 73/3918 | 203/18723 | 5.08e-07 | 1.88e-05 | 73 |
GO:0052126 | Colorectum | AD | movement in host environment | 63/3918 | 175/18723 | 2.85e-06 | 8.11e-05 | 63 |
GO:0046718 | Colorectum | AD | viral entry into host cell | 51/3918 | 144/18723 | 3.99e-05 | 7.16e-04 | 51 |
GO:0044409 | Colorectum | AD | entry into host | 51/3918 | 151/18723 | 1.60e-04 | 2.21e-03 | 51 |
GO:0010508 | Colorectum | AD | positive regulation of autophagy | 43/3918 | 124/18723 | 2.64e-04 | 3.27e-03 | 43 |
GO:0051651 | Colorectum | AD | maintenance of location in cell | 61/3918 | 214/18723 | 5.02e-03 | 3.37e-02 | 61 |
GO:00160321 | Colorectum | SER | viral process | 118/2897 | 415/18723 | 8.36e-12 | 1.65e-09 | 118 |
GO:00098961 | Colorectum | SER | positive regulation of catabolic process | 132/2897 | 492/18723 | 4.16e-11 | 6.72e-09 | 132 |
GO:00313311 | Colorectum | SER | positive regulation of cellular catabolic process | 114/2897 | 427/18723 | 1.22e-09 | 1.27e-07 | 114 |
GO:00190581 | Colorectum | SER | viral life cycle | 87/2897 | 317/18723 | 2.82e-08 | 1.94e-06 | 87 |
GO:00517011 | Colorectum | SER | biological process involved in interaction with host | 55/2897 | 203/18723 | 1.42e-05 | 4.38e-04 | 55 |
GO:00444031 | Colorectum | SER | biological process involved in symbiotic interaction | 72/2897 | 290/18723 | 2.08e-05 | 6.02e-04 | 72 |
GO:00521261 | Colorectum | SER | movement in host environment | 47/2897 | 175/18723 | 7.30e-05 | 1.64e-03 | 47 |
GO:00105061 | Colorectum | SER | regulation of autophagy | 74/2897 | 317/18723 | 1.39e-04 | 2.77e-03 | 74 |
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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 |
TPCN1 | SNV | Missense_Mutation | novel | c.511N>A | p.Ala171Thr | p.A171T | Q9ULQ1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
TPCN1 | SNV | Missense_Mutation | novel | c.2591N>A | p.Arg864Gln | p.R864Q | Q9ULQ1 | protein_coding | tolerated(0.68) | benign(0) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
TPCN1 | SNV | Missense_Mutation | rs368144508 | c.1108G>A | p.Val370Ile | p.V370I | Q9ULQ1 | protein_coding | tolerated(0.5) | benign(0.013) | TCGA-D5-7000-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
TPCN1 | SNV | Missense_Mutation | c.1091G>A | p.Arg364Gln | p.R364Q | Q9ULQ1 | protein_coding | tolerated(0.25) | benign(0.079) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD | |
TPCN1 | SNV | Missense_Mutation | c.781G>A | p.Val261Met | p.V261M | Q9ULQ1 | protein_coding | deleterious(0) | possibly_damaging(0.904) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
TPCN1 | SNV | Missense_Mutation | c.1027G>A | p.Val343Ile | p.V343I | Q9ULQ1 | protein_coding | tolerated(0.13) | benign(0.042) | TCGA-QG-A5YX-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
TPCN1 | deletion | Frame_Shift_Del | novel | c.1260delG | p.Leu421SerfsTer26 | p.L421Sfs*26 | Q9ULQ1 | protein_coding | TCGA-AA-3939-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
TPCN1 | SNV | Missense_Mutation | novel | c.1635N>T | p.Lys545Asn | p.K545N | Q9ULQ1 | protein_coding | tolerated(0.29) | benign(0.281) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
TPCN1 | SNV | Missense_Mutation | rs746208458 | c.241G>A | p.Val81Met | p.V81M | Q9ULQ1 | protein_coding | deleterious_low_confidence(0.03) | benign(0.334) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
TPCN1 | SNV | Missense_Mutation | novel | c.1802T>C | p.Met601Thr | p.M601T | Q9ULQ1 | protein_coding | tolerated(0.11) | benign(0.291) | TCGA-A5-A1OF-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 |
53373 | TPCN1 | ION CHANNEL, DRUGGABLE GENOME | blocker | 135652732 | ||
53373 | TPCN1 | ION CHANNEL, DRUGGABLE GENOME | blocker | 135651305 | VERAPAMIL | |
53373 | TPCN1 | ION CHANNEL, DRUGGABLE GENOME | activator | 178100233 |
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