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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 | SNV | Missense_Mutation | rs754671678 | c.1430C>T | p.Thr477Ile | p.T477I | P07197 | protein_coding | deleterious(0.01) | benign(0.014) | TCGA-EY-A1GO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
NEFM | SNV | Missense_Mutation | c.638C>T | p.Ala213Val | p.A213V | P07197 | protein_coding | deleterious(0) | benign(0.195) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD | |
NEFM | SNV | Missense_Mutation | novel | c.1651G>C | p.Gly551Arg | p.G551R | P07197 | protein_coding | deleterious(0.01) | possibly_damaging(0.593) | TCGA-DD-AADS-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | c.1440N>T | p.Leu480Phe | p.L480F | P07197 | protein_coding | tolerated(0.15) | benign(0.019) | TCGA-55-8094-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
NEFM | SNV | Missense_Mutation | novel | c.1441N>T | p.Ala481Ser | p.A481S | P07197 | protein_coding | tolerated(0.28) | benign(0.033) | TCGA-55-8094-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | rs140995374 | c.2635N>A | p.Val879Ile | p.V879I | P07197 | protein_coding | deleterious_low_confidence(0) | benign(0.114) | TCGA-95-7567-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD |
NEFM | SNV | Missense_Mutation | c.2384N>A | p.Ser795Tyr | p.S795Y | P07197 | protein_coding | deleterious_low_confidence(0) | benign(0.007) | TCGA-18-3416-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
NEFM | SNV | Missense_Mutation | c.220N>T | p.Ser74Cys | p.S74C | P07197 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-21-1070-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
NEFM | SNV | Missense_Mutation | novel | c.1222N>A | p.Glu408Lys | p.E408K | P07197 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-22-4594-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NEFM | SNV | Missense_Mutation | c.2147N>T | p.Glu716Val | p.E716V | P07197 | protein_coding | tolerated(0.28) | possibly_damaging(0.527) | TCGA-34-5234-01 | Lung | lung squamous cell 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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