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Gene: NOM1 |
Gene summary for NOM1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NOM1 | Gene ID | 64434 |
Gene name | nucleolar protein with MIF4G domain 1 | |
Gene Alias | C7orf3 | |
Cytomap | 7q36.3 | |
Gene Type | protein-coding | GO ID | GO:0001942 | UniProtAcc | Q5C9Z4 |
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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 |
64434 | NOM1 | HCC2 | Human | Liver | HCC | 1.44e-18 | 3.64e+00 | 0.5341 |
64434 | NOM1 | HCC5 | Human | Liver | HCC | 9.38e-09 | 1.85e+00 | 0.4932 |
64434 | NOM1 | S014 | Human | Liver | HCC | 8.03e-05 | 3.28e-01 | 0.2254 |
64434 | NOM1 | S015 | Human | Liver | HCC | 2.28e-06 | 3.07e-01 | 0.2375 |
64434 | NOM1 | S016 | Human | Liver | HCC | 7.30e-08 | 3.64e-01 | 0.2243 |
64434 | NOM1 | S027 | Human | Liver | HCC | 1.21e-03 | 5.00e-01 | 0.2446 |
64434 | NOM1 | S028 | Human | Liver | HCC | 5.39e-13 | 5.18e-01 | 0.2503 |
64434 | NOM1 | S029 | Human | Liver | HCC | 3.70e-09 | 3.83e-01 | 0.2581 |
64434 | NOM1 | C04 | Human | Oral cavity | OSCC | 1.14e-15 | 9.86e-01 | 0.2633 |
64434 | NOM1 | C21 | Human | Oral cavity | OSCC | 5.71e-06 | 4.56e-01 | 0.2678 |
64434 | NOM1 | C30 | Human | Oral cavity | OSCC | 6.38e-07 | 5.87e-01 | 0.3055 |
64434 | NOM1 | C43 | Human | Oral cavity | OSCC | 9.79e-11 | 2.74e-01 | 0.1704 |
64434 | NOM1 | C46 | Human | Oral cavity | OSCC | 1.35e-03 | 1.95e-01 | 0.1673 |
64434 | NOM1 | C51 | Human | Oral cavity | OSCC | 3.19e-06 | 5.61e-01 | 0.2674 |
64434 | NOM1 | C57 | Human | Oral cavity | OSCC | 3.50e-03 | 2.93e-01 | 0.1679 |
64434 | NOM1 | C08 | Human | Oral cavity | OSCC | 9.96e-13 | 2.90e-01 | 0.1919 |
64434 | NOM1 | LN46 | Human | Oral cavity | OSCC | 1.01e-04 | 3.45e-01 | 0.1666 |
64434 | NOM1 | SYSMH2 | Human | Oral cavity | OSCC | 1.19e-15 | 4.44e-01 | 0.2326 |
64434 | NOM1 | SYSMH3 | Human | Oral cavity | OSCC | 7.29e-19 | 4.58e-01 | 0.2442 |
64434 | NOM1 | male-WTA | Human | Thyroid | PTC | 9.40e-04 | 7.45e-02 | 0.1037 |
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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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
GO:00435888 | Esophagus | ESCC | skin development | 163/8552 | 263/18723 | 6.48e-08 | 1.14e-06 | 163 |
GO:000854410 | Esophagus | ESCC | epidermis development | 193/8552 | 324/18723 | 2.87e-07 | 4.19e-06 | 193 |
GO:00224043 | Esophagus | ESCC | molting cycle process | 53/8552 | 84/18723 | 9.62e-04 | 4.88e-03 | 53 |
GO:00224053 | Esophagus | ESCC | hair cycle process | 53/8552 | 84/18723 | 9.62e-04 | 4.88e-03 | 53 |
GO:0001942 | Esophagus | ESCC | hair follicle development | 51/8552 | 81/18723 | 1.27e-03 | 6.14e-03 | 51 |
GO:0098773 | Esophagus | ESCC | skin epidermis development | 53/8552 | 85/18723 | 1.43e-03 | 6.77e-03 | 53 |
GO:00423033 | Esophagus | ESCC | molting cycle | 64/8552 | 107/18723 | 2.24e-03 | 9.85e-03 | 64 |
GO:00426333 | Esophagus | ESCC | hair cycle | 64/8552 | 107/18723 | 2.24e-03 | 9.85e-03 | 64 |
GO:00488201 | Esophagus | ESCC | hair follicle maturation | 11/8552 | 13/18723 | 4.76e-03 | 1.85e-02 | 11 |
GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
GO:004227422 | Liver | HCC | ribosomal small subunit biogenesis | 65/7958 | 73/18723 | 1.09e-16 | 9.92e-15 | 65 |
GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
GO:004225420 | Oral cavity | OSCC | ribosome biogenesis | 230/7305 | 299/18723 | 3.22e-41 | 6.80e-38 | 230 |
GO:004227420 | Oral cavity | OSCC | ribosomal small subunit biogenesis | 63/7305 | 73/18723 | 7.61e-17 | 6.34e-15 | 63 |
GO:00435887 | Oral cavity | OSCC | skin development | 143/7305 | 263/18723 | 2.77e-07 | 4.27e-06 | 143 |
GO:00085449 | Oral cavity | OSCC | epidermis development | 171/7305 | 324/18723 | 2.89e-07 | 4.43e-06 | 171 |
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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 |
NOM1 | SNV | Missense_Mutation | novel | c.539A>G | p.Glu180Gly | p.E180G | Q5C9Z4 | protein_coding | deleterious(0.02) | probably_damaging(0.973) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
NOM1 | SNV | Missense_Mutation | rs371030013 | c.2047G>A | p.Asp683Asn | p.D683N | Q5C9Z4 | protein_coding | tolerated(0.2) | benign(0.268) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
NOM1 | insertion | Frame_Shift_Ins | novel | c.1240_1241insAGTGCTGGGATTACCGACATGAGCCACCG | p.Met414LysfsTer15 | p.M414Kfs*15 | Q5C9Z4 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
NOM1 | insertion | Frame_Shift_Ins | novel | c.1133_1134insG | p.Ser379PhefsTer20 | p.S379Ffs*20 | Q5C9Z4 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
NOM1 | insertion | In_Frame_Ins | novel | c.1134_1135insGGAATTGCCTGCATTTCCTTC | p.Ala378_Ser379insGlyIleAlaCysIleSerPhe | p.A378_S379insGIACISF | Q5C9Z4 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
NOM1 | SNV | Missense_Mutation | c.1899N>C | p.Gln633His | p.Q633H | Q5C9Z4 | protein_coding | tolerated(0.16) | benign(0.022) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | |
NOM1 | SNV | Missense_Mutation | c.1815G>C | p.Gln605His | p.Q605H | Q5C9Z4 | protein_coding | deleterious(0.03) | benign(0.009) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NOM1 | SNV | Missense_Mutation | c.2157G>C | p.Arg719Ser | p.R719S | Q5C9Z4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NOM1 | insertion | Nonsense_Mutation | novel | c.1726_1727insCAGCCTTTAGGT | p.Lys576delinsThrAlaPheArgTer | p.K576delinsTAFR* | Q5C9Z4 | protein_coding | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | ||
NOM1 | SNV | Missense_Mutation | c.2116N>C | p.Phe706Leu | p.F706L | Q5C9Z4 | protein_coding | deleterious(0.02) | benign(0.194) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | 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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