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Gene: TRAPPC9 |
Gene summary for TRAPPC9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TRAPPC9 | Gene ID | 83696 |
| Gene name | trafficking protein particle complex subunit 9 | |
| Gene Alias | IBP | |
| Cytomap | 8q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q96Q05 |
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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 |
| 83696 | TRAPPC9 | CCI_1 | Human | Cervix | CC | 5.73e-10 | 8.66e-01 | 0.528 |
| 83696 | TRAPPC9 | CCI_2 | Human | Cervix | CC | 4.71e-14 | 1.35e+00 | 0.5249 |
| 83696 | TRAPPC9 | CCI_3 | Human | Cervix | CC | 4.71e-12 | 1.11e+00 | 0.516 |
| 83696 | TRAPPC9 | CCII_1 | Human | Cervix | CC | 2.30e-05 | 3.75e-01 | 0.3249 |
| 83696 | TRAPPC9 | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.97e-19 | -6.43e-01 | 0.0155 |
| 83696 | TRAPPC9 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.50e-02 | -4.10e-01 | -0.1207 |
| 83696 | TRAPPC9 | HTA11_7862_2000001011 | Human | Colorectum | AD | 9.50e-03 | -4.48e-01 | -0.0179 |
| 83696 | TRAPPC9 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.41e-05 | -4.62e-01 | 0.096 |
| 83696 | TRAPPC9 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.62e-12 | -5.28e-01 | 0.294 |
| 83696 | TRAPPC9 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.08e-05 | 5.94e-01 | 0.281 |
| 83696 | TRAPPC9 | F007 | Human | Colorectum | FAP | 2.32e-04 | -2.14e-01 | 0.1176 |
| 83696 | TRAPPC9 | A002-C-010 | Human | Colorectum | FAP | 1.75e-02 | -8.56e-02 | 0.242 |
| 83696 | TRAPPC9 | A001-C-207 | Human | Colorectum | FAP | 1.86e-05 | -2.58e-01 | 0.1278 |
| 83696 | TRAPPC9 | A015-C-203 | Human | Colorectum | FAP | 1.62e-35 | -6.29e-01 | -0.1294 |
| 83696 | TRAPPC9 | A015-C-204 | Human | Colorectum | FAP | 9.57e-10 | -3.67e-01 | -0.0228 |
| 83696 | TRAPPC9 | A014-C-040 | Human | Colorectum | FAP | 1.88e-07 | -2.26e-01 | -0.1184 |
| 83696 | TRAPPC9 | A002-C-201 | Human | Colorectum | FAP | 1.14e-16 | -3.48e-01 | 0.0324 |
| 83696 | TRAPPC9 | A001-C-119 | Human | Colorectum | FAP | 3.74e-11 | -3.71e-01 | -0.1557 |
| 83696 | TRAPPC9 | A001-C-108 | Human | Colorectum | FAP | 6.28e-13 | -2.96e-01 | -0.0272 |
| 83696 | TRAPPC9 | A002-C-205 | Human | Colorectum | FAP | 2.65e-30 | -3.10e-01 | -0.1236 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:00510908 | Esophagus | ESCC | regulation of DNA-binding transcription factor activity | 252/8552 | 440/18723 | 5.22e-07 | 6.97e-06 | 252 |
| GO:00510918 | Esophagus | ESCC | positive regulation of DNA-binding transcription factor activity | 155/8552 | 260/18723 | 3.83e-06 | 4.14e-05 | 155 |
| GO:00510926 | Esophagus | ESCC | positive regulation of NF-kappaB transcription factor activity | 91/8552 | 152/18723 | 2.91e-04 | 1.75e-03 | 91 |
| GO:00215436 | Esophagus | ESCC | pallium development | 94/8552 | 169/18723 | 5.79e-03 | 2.14e-02 | 94 |
| GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
| GO:00510913 | Liver | HCC | positive regulation of DNA-binding transcription factor activity | 131/7958 | 260/18723 | 5.98e-03 | 2.45e-02 | 131 |
| GO:00510903 | Lung | IAC | regulation of DNA-binding transcription factor activity | 76/2061 | 440/18723 | 4.44e-05 | 1.05e-03 | 76 |
| GO:00510914 | Lung | IAC | positive regulation of DNA-binding transcription factor activity | 50/2061 | 260/18723 | 5.87e-05 | 1.29e-03 | 50 |
| GO:00219872 | Lung | IAC | cerebral cortex development | 27/2061 | 114/18723 | 8.78e-05 | 1.77e-03 | 27 |
| GO:0051092 | Lung | IAC | positive regulation of NF-kappaB transcription factor activity | 32/2061 | 152/18723 | 2.25e-04 | 3.90e-03 | 32 |
| GO:00215432 | Lung | IAC | pallium development | 33/2061 | 169/18723 | 7.51e-04 | 9.82e-03 | 33 |
| GO:00309002 | Lung | IAC | forebrain development | 61/2061 | 379/18723 | 1.52e-03 | 1.61e-02 | 61 |
| GO:00510921 | Lung | AIS | positive regulation of NF-kappaB transcription factor activity | 28/1849 | 152/18723 | 8.81e-04 | 1.19e-02 | 28 |
| GO:005109011 | Lung | AIS | regulation of DNA-binding transcription factor activity | 64/1849 | 440/18723 | 1.04e-03 | 1.36e-02 | 64 |
| GO:005109111 | Lung | AIS | positive regulation of DNA-binding transcription factor activity | 41/1849 | 260/18723 | 1.77e-03 | 2.01e-02 | 41 |
| GO:003090011 | Lung | AIS | forebrain development | 55/1849 | 379/18723 | 2.37e-03 | 2.48e-02 | 55 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| TRAPPC9 | SNV | Missense_Mutation | novel | c.2367N>G | p.Ile789Met | p.I789M | Q96Q05 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-A2-A0SU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| TRAPPC9 | SNV | Missense_Mutation | rs150200902 | c.3469N>A | p.Ala1157Thr | p.A1157T | Q96Q05 | protein_coding | tolerated(0.8) | possibly_damaging(0.714) | TCGA-A7-A26G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
| TRAPPC9 | SNV | Missense_Mutation | rs750167029 | c.3572N>T | p.Ala1191Val | p.A1191V | Q96Q05 | protein_coding | tolerated(0.28) | benign(0.062) | TCGA-AC-A8OP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRAPPC9 | SNV | Missense_Mutation | rs145782440 | c.1471N>A | p.Glu491Lys | p.E491K | Q96Q05 | protein_coding | deleterious(0.01) | possibly_damaging(0.506) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TRAPPC9 | SNV | Missense_Mutation | c.2752N>A | p.Leu918Met | p.L918M | Q96Q05 | protein_coding | tolerated(0.19) | possibly_damaging(0.584) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TRAPPC9 | SNV | Missense_Mutation | c.1226N>A | p.Ile409Asn | p.I409N | Q96Q05 | protein_coding | tolerated(0.07) | possibly_damaging(0.538) | TCGA-BH-A209-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TRAPPC9 | SNV | Missense_Mutation | c.2092N>A | p.Glu698Lys | p.E698K | Q96Q05 | protein_coding | deleterious(0) | possibly_damaging(0.81) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| TRAPPC9 | SNV | Missense_Mutation | c.1186C>T | p.Leu396Phe | p.L396F | Q96Q05 | protein_coding | deleterious(0.04) | probably_damaging(0.954) | TCGA-EW-A1OV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | SD | |
| TRAPPC9 | SNV | Missense_Mutation | novel | c.116N>T | p.Ala39Val | p.A39V | Q96Q05 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-GM-A3XL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | CR |
| TRAPPC9 | insertion | In_Frame_Ins | novel | c.1903_1904insCACACGGGAACAGGGCAGCTCCTCGCCCACACAAGCACT | p.Leu635delinsProHisGlyAsnArgAlaAlaProArgProHisLysHisPhe | p.L635delinsPHGNRAAPRPHKHF | Q96Q05 | protein_coding | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | 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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