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Gene: NEB |
Gene summary for NEB |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NEB | Gene ID | 4703 |
| Gene name | nebulin | |
| Gene Alias | AMC6 | |
| Cytomap | 2q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | P20929 |
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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 |
| 4703 | NEB | HCC1_Meng | Human | Liver | HCC | 2.18e-19 | 8.18e-02 | 0.0246 |
| 4703 | NEB | HCC1 | Human | Liver | HCC | 3.11e-04 | 3.86e+00 | 0.5336 |
| 4703 | NEB | HCC2 | Human | Liver | HCC | 5.69e-12 | 2.46e+00 | 0.5341 |
| 4703 | NEB | S027 | Human | Liver | HCC | 5.88e-04 | 4.49e-01 | 0.2446 |
| 4703 | NEB | S028 | Human | Liver | HCC | 5.12e-11 | 4.92e-01 | 0.2503 |
| 4703 | NEB | S029 | Human | Liver | HCC | 6.27e-04 | 2.96e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000701510 | Cervix | CC | actin filament organization | 109/2311 | 442/18723 | 4.92e-13 | 2.45e-10 | 109 |
| GO:00605375 | Cervix | CC | muscle tissue development | 76/2311 | 403/18723 | 9.76e-05 | 1.27e-03 | 76 |
| GO:00310329 | Cervix | CC | actomyosin structure organization | 43/2311 | 196/18723 | 1.11e-04 | 1.40e-03 | 43 |
| GO:00147064 | Cervix | CC | striated muscle tissue development | 72/2311 | 384/18723 | 1.76e-04 | 2.07e-03 | 72 |
| GO:00426924 | Cervix | CC | muscle cell differentiation | 69/2311 | 384/18723 | 8.12e-04 | 7.09e-03 | 69 |
| GO:00511464 | Cervix | CC | striated muscle cell differentiation | 50/2311 | 283/18723 | 5.53e-03 | 3.19e-02 | 50 |
| GO:000701525 | Cervix | N_HPV | actin filament organization | 29/534 | 442/18723 | 3.00e-05 | 8.02e-04 | 29 |
| GO:006053722 | Cervix | N_HPV | muscle tissue development | 21/534 | 403/18723 | 6.10e-03 | 4.21e-02 | 21 |
| GO:0007015 | Colorectum | AD | actin filament organization | 167/3918 | 442/18723 | 1.65e-16 | 7.94e-14 | 167 |
| GO:0031032 | Colorectum | AD | actomyosin structure organization | 65/3918 | 196/18723 | 4.17e-05 | 7.37e-04 | 65 |
| GO:00070151 | Colorectum | SER | actin filament organization | 134/2897 | 442/18723 | 1.39e-15 | 5.70e-13 | 134 |
| GO:00310321 | Colorectum | SER | actomyosin structure organization | 45/2897 | 196/18723 | 3.60e-03 | 3.03e-02 | 45 |
| GO:00070152 | Colorectum | MSS | actin filament organization | 146/3467 | 442/18723 | 1.16e-13 | 2.67e-11 | 146 |
| GO:00310322 | Colorectum | MSS | actomyosin structure organization | 53/3467 | 196/18723 | 2.04e-03 | 1.75e-02 | 53 |
| GO:00070153 | Colorectum | MSI-H | actin filament organization | 50/1319 | 442/18723 | 6.19e-04 | 1.21e-02 | 50 |
| GO:00070154 | Colorectum | FAP | actin filament organization | 125/2622 | 442/18723 | 1.97e-15 | 3.03e-12 | 125 |
| GO:00310323 | Colorectum | FAP | actomyosin structure organization | 51/2622 | 196/18723 | 5.89e-06 | 1.88e-04 | 51 |
| GO:0055006 | Colorectum | FAP | cardiac cell development | 22/2622 | 91/18723 | 6.44e-03 | 4.01e-02 | 22 |
| GO:00070155 | Colorectum | CRC | actin filament organization | 104/2078 | 442/18723 | 4.75e-14 | 7.12e-11 | 104 |
| GO:00310324 | Colorectum | CRC | actomyosin structure organization | 45/2078 | 196/18723 | 1.49e-06 | 8.14e-05 | 45 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| NEB | SNV | Missense_Mutation | novel | c.8357N>A | p.Arg2786Lys | p.R2786K | protein_coding | tolerated(0.07) | possibly_damaging(0.826) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| NEB | SNV | Missense_Mutation | novel | c.24651G>C | p.Gln8217His | p.Q8217H | protein_coding | deleterious(0.01) | probably_damaging(0.917) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD | |
| NEB | SNV | Missense_Mutation | novel | c.16443T>G | p.Cys5481Trp | p.C5481W | protein_coding | tolerated(0.06) | probably_damaging(0.938) | TCGA-A2-A04Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| NEB | SNV | Missense_Mutation | rs778455036 | c.21581N>A | p.Thr7194Asn | p.T7194N | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-A2-A0D0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| NEB | SNV | Missense_Mutation | novel | c.21077N>A | p.Arg7026Gln | p.R7026Q | protein_coding | tolerated(0.06) | benign(0.154) | TCGA-A2-A0EV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NEB | SNV | Missense_Mutation | novel | c.22572N>C | p.Lys7524Asn | p.K7524N | protein_coding | tolerated(0.1) | possibly_damaging(0.696) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| NEB | SNV | Missense_Mutation | c.11968N>C | p.Asp3990His | p.D3990H | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| NEB | SNV | Missense_Mutation | rs778455036 | c.21581N>A | p.Thr7194Asn | p.T7194N | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD | |
| NEB | SNV | Missense_Mutation | novel | c.11092N>T | p.Ala3698Ser | p.A3698S | protein_coding | tolerated(0.06) | possibly_damaging(0.655) | TCGA-A2-A25C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| NEB | SNV | Missense_Mutation | novel | c.10363N>T | p.Ala3455Ser | p.A3455S | protein_coding | tolerated(0.09) | probably_damaging(0.99) | TCGA-A2-A25C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 |
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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 |
| Page: 1 |
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