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Gene: HSPD1 |
Gene summary for HSPD1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | HSPD1 | Gene ID | 3329 |
Gene name | heat shock protein family D (Hsp60) member 1 | |
Gene Alias | CPN60 | |
Cytomap | 2q33.1 | |
Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | A0A024R3X4 |
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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 |
3329 | HSPD1 | GSM4909277 | Human | Breast | Precancer | 1.18e-10 | 7.81e-01 | 0.0177 |
3329 | HSPD1 | GSM4909282 | Human | Breast | IDC | 4.45e-03 | -3.90e-01 | -0.0288 |
3329 | HSPD1 | GSM4909285 | Human | Breast | IDC | 1.03e-08 | 2.95e-01 | 0.21 |
3329 | HSPD1 | GSM4909286 | Human | Breast | IDC | 7.69e-12 | -3.01e-01 | 0.1081 |
3329 | HSPD1 | GSM4909293 | Human | Breast | IDC | 5.99e-07 | -7.90e-02 | 0.1581 |
3329 | HSPD1 | GSM4909294 | Human | Breast | IDC | 1.78e-02 | 4.15e-02 | 0.2022 |
3329 | HSPD1 | GSM4909296 | Human | Breast | IDC | 3.49e-11 | -4.71e-01 | 0.1524 |
3329 | HSPD1 | GSM4909297 | Human | Breast | IDC | 5.78e-17 | -3.79e-01 | 0.1517 |
3329 | HSPD1 | GSM4909298 | Human | Breast | IDC | 4.14e-13 | -5.27e-01 | 0.1551 |
3329 | HSPD1 | GSM4909299 | Human | Breast | IDC | 6.74e-07 | -3.67e-01 | 0.035 |
3329 | HSPD1 | GSM4909300 | Human | Breast | IDC | 3.31e-02 | -4.32e-01 | 0.0334 |
3329 | HSPD1 | GSM4909301 | Human | Breast | IDC | 2.22e-08 | -4.67e-01 | 0.1577 |
3329 | HSPD1 | GSM4909302 | Human | Breast | IDC | 2.92e-10 | -5.04e-01 | 0.1545 |
3329 | HSPD1 | GSM4909306 | Human | Breast | IDC | 1.67e-05 | -3.93e-01 | 0.1564 |
3329 | HSPD1 | GSM4909307 | Human | Breast | IDC | 4.74e-13 | -5.50e-01 | 0.1569 |
3329 | HSPD1 | GSM4909308 | Human | Breast | IDC | 7.15e-04 | -2.24e-01 | 0.158 |
3329 | HSPD1 | GSM4909309 | Human | Breast | IDC | 2.12e-17 | -6.48e-01 | 0.0483 |
3329 | HSPD1 | GSM4909311 | Human | Breast | IDC | 1.07e-41 | -8.00e-01 | 0.1534 |
3329 | HSPD1 | GSM4909312 | Human | Breast | IDC | 1.11e-08 | -3.93e-01 | 0.1552 |
3329 | HSPD1 | GSM4909313 | Human | Breast | IDC | 2.09e-18 | -6.72e-01 | 0.0391 |
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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:001095012 | Liver | HCC | positive regulation of endopeptidase activity | 96/7958 | 179/18723 | 1.68e-03 | 8.79e-03 | 96 |
GO:007259312 | Liver | HCC | reactive oxygen species metabolic process | 124/7958 | 239/18723 | 2.05e-03 | 1.04e-02 | 124 |
GO:005113111 | Liver | HCC | chaperone-mediated protein complex assembly | 17/7958 | 23/18723 | 2.28e-03 | 1.13e-02 | 17 |
GO:00148231 | Liver | HCC | response to activity | 45/7958 | 76/18723 | 2.42e-03 | 1.18e-02 | 45 |
GO:004578512 | Liver | HCC | positive regulation of cell adhesion | 215/7958 | 437/18723 | 2.53e-03 | 1.22e-02 | 215 |
GO:000223711 | Liver | HCC | response to molecule of bacterial origin | 181/7958 | 363/18723 | 2.58e-03 | 1.24e-02 | 181 |
GO:0002224 | Liver | HCC | toll-like receptor signaling pathway | 67/7958 | 121/18723 | 2.87e-03 | 1.34e-02 | 67 |
GO:00436271 | Liver | HCC | response to estrogen | 44/7958 | 75/18723 | 3.44e-03 | 1.55e-02 | 44 |
GO:009876012 | Liver | HCC | response to interleukin-7 | 12/7958 | 15/18723 | 3.56e-03 | 1.59e-02 | 12 |
GO:009876112 | Liver | HCC | cellular response to interleukin-7 | 12/7958 | 15/18723 | 3.56e-03 | 1.59e-02 | 12 |
GO:004328012 | Liver | HCC | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 70/7958 | 129/18723 | 4.58e-03 | 1.97e-02 | 70 |
GO:200105612 | Liver | HCC | positive regulation of cysteine-type endopeptidase activity | 79/7958 | 148/18723 | 4.82e-03 | 2.03e-02 | 79 |
GO:0002200 | Liver | HCC | somatic diversification of immune receptors | 44/7958 | 77/18723 | 6.70e-03 | 2.72e-02 | 44 |
GO:00432791 | Liver | HCC | response to alkaloid | 62/7958 | 115/18723 | 8.79e-03 | 3.42e-02 | 62 |
GO:2000378 | Liver | HCC | negative regulation of reactive oxygen species metabolic process | 31/7958 | 52/18723 | 9.52e-03 | 3.60e-02 | 31 |
GO:0016445 | Liver | HCC | somatic diversification of immunoglobulins | 38/7958 | 67/18723 | 1.32e-02 | 4.73e-02 | 38 |
GO:004440332 | Liver | Cyst | biological process involved in symbiotic interaction | 27/496 | 290/18723 | 1.67e-08 | 2.74e-06 | 27 |
GO:000697932 | Liver | Cyst | response to oxidative stress | 30/496 | 446/18723 | 3.22e-06 | 2.66e-04 | 30 |
GO:005082132 | Liver | Cyst | protein stabilization | 17/496 | 191/18723 | 1.38e-05 | 9.07e-04 | 17 |
GO:000645722 | Liver | Cyst | protein folding | 18/496 | 212/18723 | 1.48e-05 | 9.59e-04 | 18 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513414 | Breast | Precancer | Legionellosis | 19/684 | 57/8465 | 4.62e-08 | 9.12e-07 | 6.98e-07 | 19 |
hsa0541718 | Breast | Precancer | Lipid and atherosclerosis | 37/684 | 215/8465 | 7.64e-06 | 9.29e-05 | 7.12e-05 | 37 |
hsa0513415 | Breast | Precancer | Legionellosis | 19/684 | 57/8465 | 4.62e-08 | 9.12e-07 | 6.98e-07 | 19 |
hsa0541719 | Breast | Precancer | Lipid and atherosclerosis | 37/684 | 215/8465 | 7.64e-06 | 9.29e-05 | 7.12e-05 | 37 |
hsa0513422 | Breast | IDC | Legionellosis | 19/867 | 57/8465 | 1.89e-06 | 3.07e-05 | 2.29e-05 | 19 |
hsa0494014 | Breast | IDC | Type I diabetes mellitus | 12/867 | 43/8465 | 9.40e-04 | 7.28e-03 | 5.44e-03 | 12 |
hsa0541724 | Breast | IDC | Lipid and atherosclerosis | 35/867 | 215/8465 | 3.67e-03 | 2.29e-02 | 1.71e-02 | 35 |
hsa0301821 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
hsa0513432 | Breast | IDC | Legionellosis | 19/867 | 57/8465 | 1.89e-06 | 3.07e-05 | 2.29e-05 | 19 |
hsa0494015 | Breast | IDC | Type I diabetes mellitus | 12/867 | 43/8465 | 9.40e-04 | 7.28e-03 | 5.44e-03 | 12 |
hsa0541734 | Breast | IDC | Lipid and atherosclerosis | 35/867 | 215/8465 | 3.67e-03 | 2.29e-02 | 1.71e-02 | 35 |
hsa0301831 | Breast | IDC | RNA degradation | 16/867 | 79/8465 | 5.65e-03 | 3.13e-02 | 2.34e-02 | 16 |
hsa0513441 | Breast | DCIS | Legionellosis | 19/846 | 57/8465 | 1.30e-06 | 2.10e-05 | 1.55e-05 | 19 |
hsa030184 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
hsa0541744 | Breast | DCIS | Lipid and atherosclerosis | 34/846 | 215/8465 | 4.50e-03 | 2.46e-02 | 1.82e-02 | 34 |
hsa0513451 | Breast | DCIS | Legionellosis | 19/846 | 57/8465 | 1.30e-06 | 2.10e-05 | 1.55e-05 | 19 |
hsa030185 | Breast | DCIS | RNA degradation | 16/846 | 79/8465 | 4.45e-03 | 2.46e-02 | 1.82e-02 | 16 |
hsa0541754 | Breast | DCIS | Lipid and atherosclerosis | 34/846 | 215/8465 | 4.50e-03 | 2.46e-02 | 1.82e-02 | 34 |
hsa0541720 | Cervix | CC | Lipid and atherosclerosis | 65/1267 | 215/8465 | 6.47e-09 | 1.10e-07 | 6.52e-08 | 65 |
hsa0494016 | Cervix | CC | Type I diabetes mellitus | 17/1267 | 43/8465 | 7.47e-05 | 5.04e-04 | 2.98e-04 | 17 |
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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 |
HSPD1 | SNV | Missense_Mutation | c.829N>A | p.Asp277Asn | p.D277N | P10809 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
HSPD1 | SNV | Missense_Mutation | c.390N>T | p.Lys130Asn | p.K130N | P10809 | protein_coding | tolerated(0.63) | benign(0.007) | TCGA-AR-A0TW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | PD | |
HSPD1 | SNV | Missense_Mutation | c.1483N>C | p.Met495Leu | p.M495L | P10809 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | |
HSPD1 | SNV | Missense_Mutation | c.1084G>T | p.Gly362Cys | p.G362C | P10809 | protein_coding | deleterious(0.02) | probably_damaging(0.99) | TCGA-C8-A12O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
HSPD1 | SNV | Missense_Mutation | c.460G>A | p.Glu154Lys | p.E154K | P10809 | protein_coding | tolerated(0.2) | benign(0.145) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
HSPD1 | SNV | Missense_Mutation | c.764N>G | p.Gln255Arg | p.Q255R | P10809 | protein_coding | deleterious(0.02) | benign(0.019) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
HSPD1 | SNV | Missense_Mutation | rs768557320 | c.1108N>T | p.Arg370Cys | p.R370C | P10809 | protein_coding | tolerated(0.07) | benign(0.009) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
HSPD1 | SNV | Missense_Mutation | novel | c.115N>G | p.Leu39Val | p.L39V | P10809 | protein_coding | tolerated(0.22) | benign(0.206) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
HSPD1 | SNV | Missense_Mutation | c.517N>G | p.Thr173Ala | p.T173A | P10809 | protein_coding | deleterious(0.01) | benign(0.099) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
HSPD1 | SNV | Missense_Mutation | rs751104797 | c.1178G>A | p.Arg393Gln | p.R393Q | P10809 | protein_coding | deleterious(0.02) | possibly_damaging(0.634) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | 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 |
3329 | HSPD1 | DRUGGABLE GENOME, ENZYME, CELL SURFACE | CETRORELIX | CETRORELIX | 9805247 | |
3329 | HSPD1 | DRUGGABLE GENOME, ENZYME, CELL SURFACE | ATORVASTATIN | ATORVASTATIN | 15678257 | |
3329 | HSPD1 | DRUGGABLE GENOME, ENZYME, CELL SURFACE | DiaPep-277 | DIAPEP-277 |
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