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Gene: ALYREF |
Gene summary for ALYREF |
Gene summary. |
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 |
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 |
10189 | ALYREF | P2_S3_AK | Human | Skin | AK | 7.75e-06 | 1.85e-01 | -0.3287 |
10189 | ALYREF | P2_S4_SCCIS | Human | Skin | SCCIS | 8.24e-03 | 2.13e-01 | -0.3043 |
10189 | ALYREF | P4_S8_cSCC | Human | Skin | cSCC | 2.91e-03 | 2.03e-01 | -0.3095 |
10189 | ALYREF | P5_S10_cSCC | Human | Skin | cSCC | 6.33e-16 | 2.93e-01 | -0.299 |
10189 | ALYREF | P1_cSCC | Human | Skin | cSCC | 1.67e-08 | 3.93e-01 | 0.0292 |
10189 | ALYREF | P2_cSCC | Human | Skin | cSCC | 9.35e-03 | 2.31e-01 | -0.024 |
10189 | ALYREF | P4_cSCC | Human | Skin | cSCC | 9.80e-17 | 4.08e-01 | -0.00290000000000005 |
10189 | ALYREF | P10_cSCC | Human | Skin | cSCC | 7.38e-14 | 4.38e-01 | 0.1017 |
10189 | ALYREF | male-WTA | Human | Thyroid | PTC | 1.10e-47 | 4.08e-01 | 0.1037 |
10189 | ALYREF | PTC01 | Human | Thyroid | PTC | 2.17e-03 | 3.73e-02 | 0.1899 |
10189 | ALYREF | PTC04 | Human | Thyroid | PTC | 3.33e-05 | 1.21e-01 | 0.1927 |
10189 | ALYREF | PTC05 | Human | Thyroid | PTC | 6.02e-13 | 3.03e-01 | 0.2065 |
10189 | ALYREF | PTC06 | Human | Thyroid | PTC | 1.54e-20 | 5.21e-01 | 0.2057 |
10189 | ALYREF | PTC07 | Human | Thyroid | PTC | 1.48e-28 | 4.33e-01 | 0.2044 |
10189 | ALYREF | ATC08 | Human | Thyroid | ATC | 1.67e-03 | 1.89e-01 | 0.0541 |
10189 | ALYREF | ATC12 | Human | Thyroid | ATC | 9.48e-05 | 1.31e-01 | 0.34 |
10189 | ALYREF | ATC13 | Human | Thyroid | ATC | 2.35e-08 | 1.51e-01 | 0.34 |
10189 | ALYREF | ATC2 | Human | Thyroid | ATC | 2.24e-08 | 1.12e+00 | 0.34 |
10189 | ALYREF | ATC4 | Human | Thyroid | ATC | 6.55e-07 | 2.74e-01 | 0.34 |
10189 | ALYREF | ATC5 | Human | Thyroid | ATC | 6.05e-21 | 1.76e-01 | 0.34 |
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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:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
GO:0006913 | Colorectum | AD | nucleocytoplasmic transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
GO:0051169 | Colorectum | AD | nuclear transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
GO:0044403 | Colorectum | AD | biological process involved in symbiotic interaction | 99/3918 | 290/18723 | 1.02e-07 | 4.93e-06 | 99 |
GO:0051052 | Colorectum | AD | regulation of DNA metabolic process | 116/3918 | 359/18723 | 2.47e-07 | 1.00e-05 | 116 |
GO:0051701 | Colorectum | AD | biological process involved in interaction with host | 73/3918 | 203/18723 | 5.08e-07 | 1.88e-05 | 73 |
GO:0006403 | Colorectum | AD | RNA localization | 71/3918 | 201/18723 | 1.54e-06 | 4.76e-05 | 71 |
GO:0051236 | Colorectum | AD | establishment of RNA localization | 58/3918 | 166/18723 | 1.95e-05 | 4.01e-04 | 58 |
GO:0015931 | Colorectum | AD | nucleobase-containing compound transport | 73/3918 | 222/18723 | 2.02e-05 | 4.10e-04 | 73 |
GO:0050657 | Colorectum | AD | nucleic acid transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
GO:0050658 | Colorectum | AD | RNA transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
GO:0051168 | Colorectum | AD | nuclear export | 53/3918 | 154/18723 | 6.89e-05 | 1.11e-03 | 53 |
GO:0001649 | Colorectum | AD | osteoblast differentiation | 70/3918 | 229/18723 | 3.59e-04 | 4.18e-03 | 70 |
GO:0032786 | Colorectum | AD | positive regulation of DNA-templated transcription, elongation | 13/3918 | 27/18723 | 1.47e-03 | 1.25e-02 | 13 |
GO:0051028 | Colorectum | AD | mRNA transport | 42/3918 | 130/18723 | 1.57e-03 | 1.32e-02 | 42 |
GO:0006354 | Colorectum | AD | DNA-templated transcription, elongation | 31/3918 | 91/18723 | 2.46e-03 | 1.90e-02 | 31 |
GO:0001503 | Colorectum | AD | ossification | 106/3918 | 408/18723 | 7.68e-03 | 4.64e-02 | 106 |
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Enriched KEGG pathways. |
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 |
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 |
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 |
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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