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Gene: ME1 |
Gene summary for ME1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ME1 | Gene ID | 4199 |
Gene name | malic enzyme 1 | |
Gene Alias | HUMNDME | |
Cytomap | 6q14.2 | |
Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | P48163 |
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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 |
4199 | ME1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 9.72e-03 | 3.49e-01 | -0.1808 |
4199 | ME1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.61e-14 | 6.40e-01 | -0.0811 |
4199 | ME1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.81e-10 | 4.90e-01 | -0.1088 |
4199 | ME1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.99e-03 | 5.26e-01 | -0.2196 |
4199 | ME1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.40e-04 | 3.70e-01 | -0.1526 |
4199 | ME1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.76e-03 | 2.93e-01 | -0.059 |
4199 | ME1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.35e-10 | 3.61e-01 | 0.294 |
4199 | ME1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.68e-10 | 5.39e-01 | 0.281 |
4199 | ME1 | LZE2D | Human | Esophagus | HGIN | 2.51e-03 | 7.77e-01 | 0.0642 |
4199 | ME1 | LZE2T | Human | Esophagus | ESCC | 2.21e-11 | 1.25e+00 | 0.082 |
4199 | ME1 | LZE4T | Human | Esophagus | ESCC | 1.86e-38 | 1.37e+00 | 0.0811 |
4199 | ME1 | LZE7T | Human | Esophagus | ESCC | 2.15e-14 | 6.42e-01 | 0.0667 |
4199 | ME1 | LZE22T | Human | Esophagus | ESCC | 1.33e-06 | 6.21e-01 | 0.068 |
4199 | ME1 | LZE24T | Human | Esophagus | ESCC | 4.88e-13 | 3.67e-01 | 0.0596 |
4199 | ME1 | LZE21T | Human | Esophagus | ESCC | 2.20e-05 | 5.36e-01 | 0.0655 |
4199 | ME1 | P2T-E | Human | Esophagus | ESCC | 3.84e-18 | 4.00e-01 | 0.1177 |
4199 | ME1 | P4T-E | Human | Esophagus | ESCC | 1.81e-42 | 9.88e-01 | 0.1323 |
4199 | ME1 | P5T-E | Human | Esophagus | ESCC | 1.14e-17 | 3.73e-01 | 0.1327 |
4199 | ME1 | P8T-E | Human | Esophagus | ESCC | 1.62e-07 | 2.55e-01 | 0.0889 |
4199 | ME1 | P9T-E | Human | Esophagus | ESCC | 1.05e-22 | 7.34e-01 | 0.1131 |
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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:00713262 | Colorectum | MSS | cellular response to monosaccharide stimulus | 49/3467 | 154/18723 | 4.84e-05 | 8.80e-04 | 49 |
GO:00109752 | Colorectum | MSS | regulation of neuron projection development | 115/3467 | 445/18723 | 6.91e-05 | 1.20e-03 | 115 |
GO:00091422 | Colorectum | MSS | nucleoside triphosphate biosynthetic process | 31/3467 | 85/18723 | 7.07e-05 | 1.21e-03 | 31 |
GO:00092012 | Colorectum | MSS | ribonucleoside triphosphate biosynthetic process | 28/3467 | 74/18723 | 7.38e-05 | 1.23e-03 | 28 |
GO:00091322 | Colorectum | MSS | nucleoside diphosphate metabolic process | 41/3467 | 124/18723 | 7.44e-05 | 1.24e-03 | 41 |
GO:19016542 | Colorectum | MSS | response to ketone | 58/3467 | 194/18723 | 7.70e-05 | 1.28e-03 | 58 |
GO:00109502 | Colorectum | MSS | positive regulation of endopeptidase activity | 54/3467 | 179/18723 | 1.03e-04 | 1.61e-03 | 54 |
GO:00508782 | Colorectum | MSS | regulation of body fluid levels | 99/3467 | 379/18723 | 1.40e-04 | 2.07e-03 | 99 |
GO:19012932 | Colorectum | MSS | nucleoside phosphate biosynthetic process | 71/3467 | 256/18723 | 1.80e-04 | 2.56e-03 | 71 |
GO:00091652 | Colorectum | MSS | nucleotide biosynthetic process | 70/3467 | 254/18723 | 2.44e-04 | 3.34e-03 | 70 |
GO:00469392 | Colorectum | MSS | nucleotide phosphorylation | 33/3467 | 101/18723 | 4.57e-04 | 5.43e-03 | 33 |
GO:00511012 | Colorectum | MSS | regulation of DNA binding | 37/3467 | 118/18723 | 5.29e-04 | 5.99e-03 | 37 |
GO:00506731 | Colorectum | MSS | epithelial cell proliferation | 108/3467 | 437/18723 | 6.76e-04 | 7.30e-03 | 108 |
GO:00061652 | Colorectum | MSS | nucleoside diphosphate phosphorylation | 32/3467 | 99/18723 | 6.83e-04 | 7.37e-03 | 32 |
GO:00025731 | Colorectum | MSS | myeloid leukocyte differentiation | 57/3467 | 208/18723 | 1.01e-03 | 1.01e-02 | 57 |
GO:00433882 | Colorectum | MSS | positive regulation of DNA binding | 20/3467 | 56/18723 | 1.75e-03 | 1.55e-02 | 20 |
GO:00075892 | Colorectum | MSS | body fluid secretion | 29/3467 | 93/18723 | 2.21e-03 | 1.84e-02 | 29 |
GO:00094101 | Colorectum | MSS | response to xenobiotic stimulus | 110/3467 | 462/18723 | 2.36e-03 | 1.92e-02 | 110 |
GO:00073461 | Colorectum | MSS | regulation of mitotic cell cycle | 108/3467 | 457/18723 | 3.30e-03 | 2.50e-02 | 108 |
GO:19037061 | Colorectum | MSS | regulation of hemopoiesis | 89/3467 | 367/18723 | 3.39e-03 | 2.56e-02 | 89 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa01200 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa00620 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa012001 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa006201 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa006202 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
hsa012002 | Colorectum | SER | Carbon metabolism | 40/1580 | 115/8465 | 2.77e-05 | 3.41e-04 | 2.47e-04 | 40 |
hsa006203 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
hsa012003 | Colorectum | SER | Carbon metabolism | 40/1580 | 115/8465 | 2.77e-05 | 3.41e-04 | 2.47e-04 | 40 |
hsa006204 | Colorectum | MSS | Pyruvate metabolism | 24/1875 | 47/8465 | 1.25e-05 | 1.35e-04 | 8.27e-05 | 24 |
hsa012004 | Colorectum | MSS | Carbon metabolism | 43/1875 | 115/8465 | 1.37e-04 | 1.17e-03 | 7.19e-04 | 43 |
hsa006205 | Colorectum | MSS | Pyruvate metabolism | 24/1875 | 47/8465 | 1.25e-05 | 1.35e-04 | 8.27e-05 | 24 |
hsa012005 | Colorectum | MSS | Carbon metabolism | 43/1875 | 115/8465 | 1.37e-04 | 1.17e-03 | 7.19e-04 | 43 |
hsa0062010 | Esophagus | HGIN | Pyruvate metabolism | 16/1383 | 47/8465 | 2.27e-03 | 1.95e-02 | 1.55e-02 | 16 |
hsa0120016 | Esophagus | HGIN | Carbon metabolism | 31/1383 | 115/8465 | 2.51e-03 | 2.10e-02 | 1.67e-02 | 31 |
hsa0062013 | Esophagus | HGIN | Pyruvate metabolism | 16/1383 | 47/8465 | 2.27e-03 | 1.95e-02 | 1.55e-02 | 16 |
hsa0120017 | Esophagus | HGIN | Carbon metabolism | 31/1383 | 115/8465 | 2.51e-03 | 2.10e-02 | 1.67e-02 | 31 |
hsa0120023 | Esophagus | ESCC | Carbon metabolism | 79/4205 | 115/8465 | 2.50e-05 | 1.21e-04 | 6.22e-05 | 79 |
hsa0062023 | Esophagus | ESCC | Pyruvate metabolism | 32/4205 | 47/8465 | 8.11e-03 | 1.94e-02 | 9.94e-03 | 32 |
hsa0120033 | Esophagus | ESCC | Carbon metabolism | 79/4205 | 115/8465 | 2.50e-05 | 1.21e-04 | 6.22e-05 | 79 |
hsa0062033 | Esophagus | ESCC | Pyruvate metabolism | 32/4205 | 47/8465 | 8.11e-03 | 1.94e-02 | 9.94e-03 | 32 |
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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 |
ME1 | SNV | Missense_Mutation | novel | c.181A>C | p.Asn61His | p.N61H | P48163 | protein_coding | deleterious(0.02) | possibly_damaging(0.787) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ME1 | SNV | Missense_Mutation | c.1364N>A | p.Ser455Tyr | p.S455Y | P48163 | protein_coding | deleterious(0.02) | probably_damaging(0.967) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
ME1 | SNV | Missense_Mutation | c.1696N>G | p.Ile566Val | p.I566V | P48163 | protein_coding | tolerated_low_confidence(1) | benign(0) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
ME1 | SNV | Missense_Mutation | c.455N>T | p.Asp152Val | p.D152V | P48163 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
ME1 | SNV | Missense_Mutation | rs775383665 | c.1030C>T | p.Arg344Cys | p.R344C | P48163 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-3842-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | PD |
ME1 | SNV | Missense_Mutation | novel | c.1688T>C | p.Val563Ala | p.V563A | P48163 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ME1 | SNV | Missense_Mutation | c.200N>T | p.Ser67Phe | p.S67F | P48163 | protein_coding | deleterious(0.02) | possibly_damaging(0.624) | TCGA-AA-3973-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Targeted Molecular therapy | bevacizumab | SD | |
ME1 | SNV | Missense_Mutation | c.133N>A | p.Pro45Thr | p.P45T | P48163 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A01I-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
ME1 | SNV | Missense_Mutation | rs868866711 | c.385N>A | p.Asp129Asn | p.D129N | P48163 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ME1 | SNV | Missense_Mutation | novel | c.178N>C | p.Lys60Gln | p.K60Q | P48163 | protein_coding | tolerated(0.47) | benign(0.051) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
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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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