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Gene: NEFM |
Gene summary for NEFM |
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Gene information | Species | Human | Gene symbol | NEFM | Gene ID | 4741 |
Gene name | neurofilament medium chain | |
Gene Alias | NEF3 | |
Cytomap | 8p21.2 | |
Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | Q9UK51 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
4741 | NEFM | P5T-E | Human | Esophagus | ESCC | 1.54e-08 | 4.19e-01 | 0.1327 |
4741 | NEFM | P10T-E | Human | Esophagus | ESCC | 5.12e-07 | 1.88e-01 | 0.116 |
4741 | NEFM | P24T-E | Human | Esophagus | ESCC | 3.43e-04 | 1.14e-01 | 0.1287 |
4741 | NEFM | P26T-E | Human | Esophagus | ESCC | 9.64e-05 | 1.95e-01 | 0.1276 |
4741 | NEFM | P30T-E | Human | Esophagus | ESCC | 4.55e-14 | 1.16e+00 | 0.137 |
4741 | NEFM | P36T-E | Human | Esophagus | ESCC | 3.91e-06 | 8.26e-01 | 0.1187 |
4741 | NEFM | P47T-E | Human | Esophagus | ESCC | 1.51e-08 | 2.23e-01 | 0.1067 |
4741 | NEFM | P107T-E | Human | Esophagus | ESCC | 1.54e-74 | 3.06e+00 | 0.171 |
4741 | NEFM | P1_cSCC | Human | Skin | cSCC | 2.52e-18 | 1.22e+00 | 0.0292 |
4741 | NEFM | P10_cSCC | Human | Skin | cSCC | 6.21e-29 | 1.64e+00 | 0.1017 |
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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:00451035 | Esophagus | ESCC | intermediate filament-based process | 32/8552 | 52/18723 | 1.55e-02 | 4.97e-02 | 32 |
GO:004510423 | Skin | cSCC | intermediate filament cytoskeleton organization | 24/4864 | 51/18723 | 9.43e-04 | 6.42e-03 | 24 |
GO:004510323 | Skin | cSCC | intermediate filament-based process | 24/4864 | 52/18723 | 1.32e-03 | 8.50e-03 | 24 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
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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 |
NEFM | insertion | Frame_Shift_Ins | novel | c.2581dupA | p.Ile861AsnfsTer4 | p.I861Nfs*4 | P07197 | protein_coding | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
NEFM | SNV | Missense_Mutation | c.127G>A | p.Gly43Ser | p.G43S | P07197 | protein_coding | tolerated(0.39) | benign(0.019) | TCGA-A5-A0GB-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NEFM | SNV | Missense_Mutation | novel | c.619C>T | p.Arg207Cys | p.R207C | P07197 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | novel | c.1355T>G | p.Phe452Cys | p.F452C | P07197 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | novel | c.319G>A | p.Gly107Arg | p.G107R | P07197 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | novel | c.1901N>T | p.Pro634Leu | p.P634L | P07197 | protein_coding | deleterious(0.05) | benign(0.022) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
NEFM | SNV | Missense_Mutation | novel | c.1804N>A | p.Val602Met | p.V602M | P07197 | protein_coding | tolerated(0.11) | benign(0.111) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | novel | c.1523C>T | p.Ala508Val | p.A508V | P07197 | protein_coding | tolerated(0.11) | benign(0.1) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | c.194N>T | p.Ser65Leu | p.S65L | P07197 | protein_coding | deleterious(0.03) | benign(0.013) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
NEFM | SNV | Missense_Mutation | c.1384N>T | p.Val462Leu | p.V462L | P07197 | protein_coding | deleterious(0.03) | possibly_damaging(0.745) | TCGA-AP-A059-01 | 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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