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Gene: ALYREF |
Gene summary for ALYREF |
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Gene information | Species | Human | Gene symbol | ALYREF | Gene ID | 10189 |
Gene name | Aly/REF export factor | |
Gene Alias | ALY | |
Cytomap | 17q25.3 | |
Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | E9PB61 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
10189 | ALYREF | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.80e-07 | 2.20e-01 | -0.1808 |
10189 | ALYREF | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.85e-14 | 4.77e-01 | -0.0811 |
10189 | ALYREF | HTA11_78_2000001011 | Human | Colorectum | AD | 6.11e-04 | 1.33e-01 | -0.1088 |
10189 | ALYREF | HTA11_347_2000001011 | Human | Colorectum | AD | 1.11e-09 | 2.32e-01 | -0.1954 |
10189 | ALYREF | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.09e-06 | 3.17e-01 | -0.1207 |
10189 | ALYREF | HTA11_83_2000001011 | Human | Colorectum | SER | 2.04e-02 | 1.36e-01 | -0.1526 |
10189 | ALYREF | HTA11_696_2000001011 | Human | Colorectum | AD | 1.74e-10 | 3.14e-01 | -0.1464 |
10189 | ALYREF | HTA11_866_2000001011 | Human | Colorectum | AD | 6.14e-04 | 1.76e-01 | -0.1001 |
10189 | ALYREF | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.99e-16 | 4.02e-01 | -0.059 |
10189 | ALYREF | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.14e-07 | 3.66e-01 | -0.1706 |
10189 | ALYREF | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.47e-08 | 2.92e-01 | -0.0179 |
10189 | ALYREF | HTA11_866_3004761011 | Human | Colorectum | AD | 1.85e-21 | 4.78e-01 | 0.096 |
10189 | ALYREF | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.40e-02 | 2.39e-01 | 0.0446 |
10189 | ALYREF | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.13e-05 | 2.34e-01 | 0.0528 |
10189 | ALYREF | HTA11_10623_2000001011 | Human | Colorectum | AD | 2.05e-04 | 1.94e-01 | -0.0177 |
10189 | ALYREF | HTA11_6801_2000001011 | Human | Colorectum | SER | 3.07e-13 | 7.02e-01 | 0.0171 |
10189 | ALYREF | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.91e-07 | 2.27e-01 | 0.0338 |
10189 | ALYREF | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.20e-16 | 3.95e-01 | 0.0674 |
10189 | ALYREF | HTA11_7469_2000001011 | Human | Colorectum | AD | 2.51e-08 | 4.42e-01 | -0.0124 |
10189 | ALYREF | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.54e-06 | 2.06e-01 | 0.0588 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00003752 | Colorectum | MSS | RNA splicing, via transesterification reactions | 122/3467 | 324/18723 | 2.75e-16 | 8.58e-14 | 122 |
GO:00069132 | Colorectum | MSS | nucleocytoplasmic transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
GO:00511692 | Colorectum | MSS | nuclear transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
GO:00444032 | Colorectum | MSS | biological process involved in symbiotic interaction | 93/3467 | 290/18723 | 1.72e-08 | 9.85e-07 | 93 |
GO:00510522 | Colorectum | MSS | regulation of DNA metabolic process | 108/3467 | 359/18723 | 5.86e-08 | 3.10e-06 | 108 |
GO:00064032 | Colorectum | MSS | RNA localization | 69/3467 | 201/18723 | 6.33e-08 | 3.26e-06 | 69 |
GO:00517012 | Colorectum | MSS | biological process involved in interaction with host | 67/3467 | 203/18723 | 5.13e-07 | 1.98e-05 | 67 |
GO:00159312 | Colorectum | MSS | nucleobase-containing compound transport | 70/3467 | 222/18723 | 1.92e-06 | 6.01e-05 | 70 |
GO:00512362 | Colorectum | MSS | establishment of RNA localization | 55/3467 | 166/18723 | 4.54e-06 | 1.27e-04 | 55 |
GO:00506572 | Colorectum | MSS | nucleic acid transport | 54/3467 | 163/18723 | 5.54e-06 | 1.49e-04 | 54 |
GO:00506582 | Colorectum | MSS | RNA transport | 54/3467 | 163/18723 | 5.54e-06 | 1.49e-04 | 54 |
GO:00511682 | Colorectum | MSS | nuclear export | 51/3467 | 154/18723 | 1.01e-05 | 2.43e-04 | 51 |
GO:00016492 | Colorectum | MSS | osteoblast differentiation | 64/3467 | 229/18723 | 2.91e-04 | 3.83e-03 | 64 |
GO:00510281 | Colorectum | MSS | mRNA transport | 40/3467 | 130/18723 | 4.94e-04 | 5.75e-03 | 40 |
GO:00063541 | Colorectum | MSS | DNA-templated transcription, elongation | 29/3467 | 91/18723 | 1.52e-03 | 1.39e-02 | 29 |
GO:00327861 | Colorectum | MSS | positive regulation of DNA-templated transcription, elongation | 12/3467 | 27/18723 | 1.74e-03 | 1.55e-02 | 12 |
GO:0006405 | Colorectum | MSS | RNA export from nucleus | 27/3467 | 84/18723 | 1.89e-03 | 1.66e-02 | 27 |
GO:00015032 | Colorectum | MSS | ossification | 96/3467 | 408/18723 | 6.09e-03 | 4.07e-02 | 96 |
GO:0006406 | Colorectum | MSS | mRNA export from nucleus | 19/3467 | 59/18723 | 8.19e-03 | 4.97e-02 | 19 |
GO:0071427 | Colorectum | MSS | mRNA-containing ribonucleoprotein complex export from nucleus | 19/3467 | 59/18723 | 8.19e-03 | 4.97e-02 | 19 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
hsa03015 | Colorectum | AD | mRNA surveillance pathway | 35/2092 | 97/8465 | 7.95e-03 | 3.13e-02 | 2.00e-02 | 35 |
hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
hsa030151 | Colorectum | AD | mRNA surveillance pathway | 35/2092 | 97/8465 | 7.95e-03 | 3.13e-02 | 2.00e-02 | 35 |
hsa050142 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
hsa050143 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
hsa050144 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
hsa050145 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
hsa050146 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
hsa050147 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
ALYREF | insertion | In_Frame_Ins | novel | c.496_497insATG | p.Asp165dup | p.D165dup | protein_coding | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |||
ALYREF | SNV | Missense_Mutation | novel | c.626N>C | p.Arg209Thr | p.R209T | protein_coding | tolerated(0.34) | benign(0.028) | TCGA-EA-A78R-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
ALYREF | SNV | Missense_Mutation | c.526G>A | p.Val176Ile | p.V176I | protein_coding | tolerated(0.11) | possibly_damaging(0.516) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
ALYREF | SNV | Missense_Mutation | novel | c.535G>C | p.Asp179His | p.D179H | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-G4-6295-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
ALYREF | SNV | Missense_Mutation | c.712G>A | p.Gly238Ser | p.G238S | protein_coding | tolerated(0.12) | possibly_damaging(0.576) | TCGA-EI-6508-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | ||
ALYREF | SNV | Missense_Mutation | novel | c.353N>T | p.Ser118Phe | p.S118F | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-4E-A92E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
ALYREF | SNV | Missense_Mutation | novel | c.413N>T | p.Thr138Met | p.T138M | protein_coding | deleterious(0.02) | possibly_damaging(0.82) | TCGA-AJ-A3NE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
ALYREF | SNV | Missense_Mutation | novel | c.428N>T | p.Ala143Val | p.A143V | protein_coding | deleterious(0) | possibly_damaging(0.871) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
ALYREF | SNV | Missense_Mutation | rs781729860 | c.586N>T | p.Arg196Trp | p.R196W | protein_coding | deleterious(0.05) | probably_damaging(0.983) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
ALYREF | SNV | Missense_Mutation | novel | c.575N>G | p.Ile192Ser | p.I192S | protein_coding | deleterious(0) | benign(0.048) | TCGA-AP-A1DM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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