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Gene: EMD |
Gene summary for EMD |
Gene summary. |
Gene information | Species | Human | Gene symbol | EMD | Gene ID | 2010 |
Gene name | emerin | |
Gene Alias | EDMD | |
Cytomap | Xq28 | |
Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | P50402 |
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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 |
2010 | EMD | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.33e-04 | 1.55e-01 | 0.0155 |
2010 | EMD | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.89e-07 | 2.87e-01 | -0.1808 |
2010 | EMD | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.87e-02 | 2.79e-01 | 0.0216 |
2010 | EMD | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.62e-02 | 1.92e-01 | -0.0811 |
2010 | EMD | HTA11_347_2000001011 | Human | Colorectum | AD | 9.56e-08 | 2.62e-01 | -0.1954 |
2010 | EMD | HTA11_411_2000001011 | Human | Colorectum | SER | 4.39e-03 | 5.71e-01 | -0.2602 |
2010 | EMD | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.66e-07 | 3.99e-01 | -0.1207 |
2010 | EMD | HTA11_696_2000001011 | Human | Colorectum | AD | 9.34e-11 | 3.22e-01 | -0.1464 |
2010 | EMD | HTA11_866_2000001011 | Human | Colorectum | AD | 9.11e-06 | 1.76e-01 | -0.1001 |
2010 | EMD | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.20e-12 | 4.34e-01 | -0.059 |
2010 | EMD | HTA11_546_2000001011 | Human | Colorectum | AD | 4.12e-04 | 3.86e-01 | -0.0842 |
2010 | EMD | HTA11_866_3004761011 | Human | Colorectum | AD | 7.05e-07 | 3.06e-01 | 0.096 |
2010 | EMD | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.20e-02 | 2.58e-01 | 0.0528 |
2010 | EMD | HTA11_7663_2000001011 | Human | Colorectum | SER | 4.64e-03 | 3.78e-01 | 0.0131 |
2010 | EMD | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.32e-03 | 2.20e-01 | 0.0338 |
2010 | EMD | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.69e-14 | 3.25e-01 | 0.0674 |
2010 | EMD | HTA11_7469_2000001011 | Human | Colorectum | AD | 9.89e-03 | 4.64e-01 | -0.0124 |
2010 | EMD | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.39e-05 | 3.90e-01 | 0.0588 |
2010 | EMD | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.63e-12 | 3.19e-01 | 0.294 |
2010 | EMD | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.42e-14 | 4.55e-01 | 0.281 |
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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:004682420 | Thyroid | PTC | positive regulation of nucleocytoplasmic transport | 47/5968 | 62/18723 | 1.44e-12 | 6.50e-11 | 47 |
GO:0030111110 | Thyroid | PTC | regulation of Wnt signaling pathway | 163/5968 | 328/18723 | 1.05e-11 | 4.29e-10 | 163 |
GO:0006611110 | Thyroid | PTC | protein export from nucleus | 43/5968 | 57/18723 | 1.73e-11 | 6.81e-10 | 43 |
GO:0046825112 | Thyroid | PTC | regulation of protein export from nucleus | 27/5968 | 30/18723 | 5.10e-11 | 1.81e-09 | 27 |
GO:0060828110 | Thyroid | PTC | regulation of canonical Wnt signaling pathway | 123/5968 | 253/18723 | 1.83e-08 | 4.26e-07 | 123 |
GO:0060070110 | Thyroid | PTC | canonical Wnt signaling pathway | 141/5968 | 303/18723 | 5.71e-08 | 1.21e-06 | 141 |
GO:004682715 | Thyroid | PTC | positive regulation of protein export from nucleus | 15/5968 | 17/18723 | 2.36e-06 | 3.13e-05 | 15 |
GO:00069977 | Thyroid | PTC | nucleus organization | 65/5968 | 133/18723 | 3.16e-05 | 3.01e-04 | 65 |
GO:00717636 | Thyroid | PTC | nuclear membrane organization | 21/5968 | 33/18723 | 1.73e-04 | 1.32e-03 | 21 |
GO:004814516 | Thyroid | PTC | regulation of fibroblast proliferation | 41/5968 | 80/18723 | 2.43e-04 | 1.75e-03 | 41 |
GO:00069985 | Thyroid | PTC | nuclear envelope organization | 27/5968 | 47/18723 | 2.57e-04 | 1.84e-03 | 27 |
GO:004814416 | Thyroid | PTC | fibroblast proliferation | 41/5968 | 81/18723 | 3.41e-04 | 2.35e-03 | 41 |
GO:003017810 | Thyroid | PTC | negative regulation of Wnt signaling pathway | 74/5968 | 170/18723 | 8.99e-04 | 5.48e-03 | 74 |
GO:006053719 | Thyroid | PTC | muscle tissue development | 156/5968 | 403/18723 | 1.98e-03 | 1.06e-02 | 156 |
GO:00900907 | Thyroid | PTC | negative regulation of canonical Wnt signaling pathway | 59/5968 | 137/18723 | 3.76e-03 | 1.80e-02 | 59 |
GO:001470617 | Thyroid | PTC | striated muscle tissue development | 144/5968 | 384/18723 | 1.05e-02 | 4.22e-02 | 144 |
GO:004814523 | Thyroid | goiters | regulation of fibroblast proliferation | 11/497 | 80/18723 | 8.28e-06 | 3.54e-04 | 11 |
GO:004814423 | Thyroid | goiters | fibroblast proliferation | 11/497 | 81/18723 | 9.36e-06 | 3.88e-04 | 11 |
GO:00481474 | Thyroid | goiters | negative regulation of fibroblast proliferation | 6/497 | 30/18723 | 1.17e-04 | 3.57e-03 | 6 |
GO:005116826 | Thyroid | goiters | nuclear export | 13/497 | 154/18723 | 2.42e-04 | 6.65e-03 | 13 |
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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 |
EMD | SNV | Missense_Mutation | c.700G>T | p.Val234Phe | p.V234F | P50402 | protein_coding | deleterious(0.02) | benign(0.235) | TCGA-AN-A0AM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
EMD | SNV | Missense_Mutation | c.173N>G | p.Ser58Cys | p.S58C | P50402 | protein_coding | tolerated(0.07) | possibly_damaging(0.75) | TCGA-C5-A1M6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
EMD | SNV | Missense_Mutation | c.720N>A | p.Phe240Leu | p.F240L | P50402 | protein_coding | tolerated(1) | benign(0) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | |
EMD | SNV | Missense_Mutation | rs782057378 | c.662N>A | p.Arg221His | p.R221H | P50402 | protein_coding | deleterious(0) | benign(0) | TCGA-AA-3662-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | capecitabine | PR |
EMD | SNV | Missense_Mutation | c.661C>T | p.Arg221Cys | p.R221C | P50402 | protein_coding | deleterious(0) | benign(0.441) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
EMD | SNV | Missense_Mutation | c.146N>T | p.Ser49Leu | p.S49L | P50402 | protein_coding | tolerated(0.12) | benign(0.005) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
EMD | SNV | Missense_Mutation | novel | c.407A>C | p.Asp136Ala | p.D136A | P50402 | protein_coding | tolerated(0.05) | benign(0.003) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
EMD | SNV | Missense_Mutation | c.610C>A | p.Arg204Ser | p.R204S | P50402 | protein_coding | deleterious(0.01) | benign(0.182) | TCGA-CK-5913-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
EMD | SNV | Missense_Mutation | c.752G>T | p.Gly251Val | p.G251V | P50402 | protein_coding | deleterious(0.01) | benign(0.298) | TCGA-AF-A56N-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
EMD | SNV | Missense_Mutation | rs782768362 | c.385N>A | p.Ala129Thr | p.A129T | P50402 | protein_coding | tolerated(1) | benign(0) | TCGA-EI-6508-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | 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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