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Gene: SPG7 |
Gene summary for SPG7 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SPG7 | Gene ID | 6687 |
Gene name | SPG7 matrix AAA peptidase subunit, paraplegin | |
Gene Alias | CAR | |
Cytomap | 16q24.3 | |
Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q9UQ90 |
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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 |
6687 | SPG7 | LZE2D | Human | Esophagus | HGIN | 3.25e-04 | 3.13e-01 | 0.0642 |
6687 | SPG7 | LZE2T | Human | Esophagus | ESCC | 5.74e-14 | 6.72e-01 | 0.082 |
6687 | SPG7 | LZE4T | Human | Esophagus | ESCC | 2.89e-14 | 4.17e-01 | 0.0811 |
6687 | SPG7 | LZE5T | Human | Esophagus | ESCC | 2.28e-07 | 4.73e-01 | 0.0514 |
6687 | SPG7 | LZE7T | Human | Esophagus | ESCC | 4.95e-13 | 8.03e-01 | 0.0667 |
6687 | SPG7 | LZE8T | Human | Esophagus | ESCC | 2.15e-12 | 3.11e-01 | 0.067 |
6687 | SPG7 | LZE20T | Human | Esophagus | ESCC | 1.39e-10 | 5.36e-01 | 0.0662 |
6687 | SPG7 | LZE21D1 | Human | Esophagus | HGIN | 2.70e-06 | 5.60e-01 | 0.0632 |
6687 | SPG7 | LZE22D1 | Human | Esophagus | HGIN | 1.16e-05 | 2.26e-01 | 0.0595 |
6687 | SPG7 | LZE22T | Human | Esophagus | ESCC | 9.39e-10 | 3.50e-01 | 0.068 |
6687 | SPG7 | LZE24T | Human | Esophagus | ESCC | 7.60e-21 | 5.89e-01 | 0.0596 |
6687 | SPG7 | LZE21T | Human | Esophagus | ESCC | 1.08e-05 | 6.60e-01 | 0.0655 |
6687 | SPG7 | P1T-E | Human | Esophagus | ESCC | 2.94e-27 | 1.13e+00 | 0.0875 |
6687 | SPG7 | P2T-E | Human | Esophagus | ESCC | 4.69e-39 | 6.42e-01 | 0.1177 |
6687 | SPG7 | P4T-E | Human | Esophagus | ESCC | 7.11e-28 | 5.98e-01 | 0.1323 |
6687 | SPG7 | P5T-E | Human | Esophagus | ESCC | 1.84e-20 | 3.62e-01 | 0.1327 |
6687 | SPG7 | P8T-E | Human | Esophagus | ESCC | 3.48e-49 | 8.01e-01 | 0.0889 |
6687 | SPG7 | P9T-E | Human | Esophagus | ESCC | 2.61e-19 | 3.97e-01 | 0.1131 |
6687 | SPG7 | P10T-E | Human | Esophagus | ESCC | 1.12e-35 | 6.01e-01 | 0.116 |
6687 | SPG7 | P11T-E | Human | Esophagus | ESCC | 4.22e-19 | 8.09e-01 | 0.1426 |
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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:000683920 | Esophagus | HGIN | mitochondrial transport | 74/2587 | 254/18723 | 1.32e-10 | 1.32e-08 | 74 |
GO:000700618 | Esophagus | HGIN | mitochondrial membrane organization | 37/2587 | 116/18723 | 4.61e-07 | 2.07e-05 | 37 |
GO:005160417 | Esophagus | HGIN | protein maturation | 68/2587 | 294/18723 | 9.77e-06 | 2.86e-04 | 68 |
GO:003070517 | Esophagus | HGIN | cytoskeleton-dependent intracellular transport | 45/2587 | 195/18723 | 3.07e-04 | 5.15e-03 | 45 |
GO:00164857 | Esophagus | HGIN | protein processing | 49/2587 | 225/18723 | 7.04e-04 | 9.52e-03 | 49 |
GO:00109707 | Esophagus | HGIN | transport along microtubule | 35/2587 | 155/18723 | 2.01e-03 | 2.12e-02 | 35 |
GO:00469029 | Esophagus | HGIN | regulation of mitochondrial membrane permeability | 17/2587 | 63/18723 | 4.29e-03 | 3.82e-02 | 17 |
GO:19026869 | Esophagus | HGIN | mitochondrial outer membrane permeabilization involved in programmed cell death | 12/2587 | 40/18723 | 6.22e-03 | 4.95e-02 | 12 |
GO:0006839110 | Esophagus | ESCC | mitochondrial transport | 187/8552 | 254/18723 | 8.35e-20 | 9.81e-18 | 187 |
GO:000700619 | Esophagus | ESCC | mitochondrial membrane organization | 93/8552 | 116/18723 | 2.16e-14 | 1.11e-12 | 93 |
GO:005160418 | Esophagus | ESCC | protein maturation | 189/8552 | 294/18723 | 7.64e-11 | 2.39e-09 | 189 |
GO:003070518 | Esophagus | ESCC | cytoskeleton-dependent intracellular transport | 133/8552 | 195/18723 | 1.48e-10 | 4.27e-09 | 133 |
GO:001097013 | Esophagus | ESCC | transport along microtubule | 107/8552 | 155/18723 | 3.17e-09 | 6.80e-08 | 107 |
GO:000808810 | Esophagus | ESCC | axo-dendritic transport | 58/8552 | 75/18723 | 2.09e-08 | 4.02e-07 | 58 |
GO:004690217 | Esophagus | ESCC | regulation of mitochondrial membrane permeability | 49/8552 | 63/18723 | 1.91e-07 | 2.97e-06 | 49 |
GO:00905599 | Esophagus | ESCC | regulation of membrane permeability | 58/8552 | 78/18723 | 2.38e-07 | 3.61e-06 | 58 |
GO:00357948 | Esophagus | ESCC | positive regulation of mitochondrial membrane permeability | 36/8552 | 43/18723 | 2.90e-07 | 4.20e-06 | 36 |
GO:00989304 | Esophagus | ESCC | axonal transport | 49/8552 | 64/18723 | 4.54e-07 | 6.15e-06 | 49 |
GO:190268614 | Esophagus | ESCC | mitochondrial outer membrane permeabilization involved in programmed cell death | 33/8552 | 40/18723 | 1.80e-06 | 2.11e-05 | 33 |
GO:19057108 | Esophagus | ESCC | positive regulation of membrane permeability | 37/8552 | 48/18723 | 8.99e-06 | 8.65e-05 | 37 |
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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 |
SPG7 | SNV | Missense_Mutation | rs753722512 | c.1600N>T | p.Arg534Trp | p.R534W | Q9UQ90 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-BR-4201-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
SPG7 | SNV | Missense_Mutation | c.719N>T | p.Arg240Met | p.R240M | Q9UQ90 | protein_coding | tolerated(0.21) | probably_damaging(0.95) | TCGA-BR-4363-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
SPG7 | SNV | Missense_Mutation | rs765608610 | c.1423G>A | p.Val475Ile | p.V475I | Q9UQ90 | protein_coding | tolerated(1) | benign(0.003) | TCGA-BR-6801-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SPG7 | SNV | Missense_Mutation | rs149437163 | c.1618G>A | p.Val540Met | p.V540M | Q9UQ90 | protein_coding | deleterious(0) | probably_damaging(0.915) | TCGA-BR-A4IZ-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SPG7 | SNV | Missense_Mutation | rs771640502 | c.1642G>A | p.Ala548Thr | p.A548T | Q9UQ90 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-F1-6177-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SPG7 | SNV | Missense_Mutation | novel | c.1625C>T | p.Thr542Ile | p.T542I | Q9UQ90 | protein_coding | tolerated(0.12) | benign(0.026) | TCGA-VQ-A8E3-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
SPG7 | SNV | Missense_Mutation | rs115999025 | c.1213N>A | p.Val405Ile | p.V405I | Q9UQ90 | protein_coding | tolerated(0.78) | benign(0.373) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
SPG7 | deletion | Frame_Shift_Del | rs764134543 | c.1047delN | p.Gly352AlafsTer87 | p.G352Afs*87 | Q9UQ90 | protein_coding | TCGA-CD-A4MG-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
SPG7 | deletion | Frame_Shift_Del | novel | c.1166delN | p.Arg389LeufsTer50 | p.R389Lfs*50 | Q9UQ90 | protein_coding | TCGA-CD-A4MJ-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR | ||
SPG7 | deletion | Frame_Shift_Del | c.1672delN | p.Lys559ArgfsTer33 | p.K559Rfs*33 | Q9UQ90 | protein_coding | TCGA-CG-4442-01 | Stomach | stomach adenocarcinoma | Male | >=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 |
6687 | SPG7 | PROTEASE, ENZYME | docetaxel | DOCETAXEL | 20038957 | |
6687 | SPG7 | PROTEASE, ENZYME | anthracyclines and related substances | 23441093,21900104 | ||
6687 | SPG7 | PROTEASE, ENZYME | thalidomide | THALIDOMIDE | 20038957 |
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