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Gene: NHP2L1 |
Gene summary for NHP2L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NHP2L1 | Gene ID | 4809 |
| Gene name | small nuclear ribonucleoprotein 13 | |
| Gene Alias | 15.5K | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P55769 |
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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 |
| 4809 | NHP2L1 | Pt13.a | Human | Liver | HCC | 7.65e-50 | 7.99e-01 | 0.021 |
| 4809 | NHP2L1 | Pt13.b | Human | Liver | HCC | 1.36e-82 | 8.76e-01 | 0.0251 |
| 4809 | NHP2L1 | Pt13.c | Human | Liver | HCC | 6.11e-10 | 4.67e-01 | 0.0076 |
| 4809 | NHP2L1 | Pt14.a | Human | Liver | HCC | 1.24e-38 | 1.13e+00 | 0.0169 |
| 4809 | NHP2L1 | Pt14.b | Human | Liver | HCC | 5.32e-40 | 9.17e-01 | 0.018 |
| 4809 | NHP2L1 | Pt14.c | Human | Liver | HCC | 1.81e-08 | 6.06e-01 | 0.0054 |
| 4809 | NHP2L1 | Pt14.d | Human | Liver | HCC | 2.58e-41 | 7.23e-01 | 0.0143 |
| 4809 | NHP2L1 | GSM5353216_PA_PB1A_Pool_1_3_S50_L002 | Human | Prostate | Tumor | 2.22e-03 | 5.01e-01 | 0.159 |
| 4809 | NHP2L1 | GSM5353218_PA_PB1B_Pool_1_2_S74_L003 | Human | Prostate | Tumor | 6.49e-08 | 7.15e-01 | 0.1479 |
| 4809 | NHP2L1 | GSM5353220_PA_PB1B_Pool_3_S51_L002 | Human | Prostate | Tumor | 3.78e-07 | 6.50e-01 | 0.1531 |
| 4809 | NHP2L1 | GSM5353221_PA_PB2A_Pool_1_3_S25_L001 | Human | Prostate | Tumor | 1.25e-17 | 5.92e-01 | 0.1633 |
| 4809 | NHP2L1 | GSM5353222_PA_PB2B_Pool_1_3_S52_L002 | Human | Prostate | Tumor | 5.46e-11 | 3.60e-01 | 0.1608 |
| 4809 | NHP2L1 | GSM5353223_PA_PB2B_Pool_2_S26_L001 | Human | Prostate | Tumor | 1.19e-11 | 4.76e-01 | 0.1604 |
| 4809 | NHP2L1 | GSM5353224_PA_PR5186_Pool_1_2_3_S27_L001 | Human | Prostate | Tumor | 2.07e-22 | 6.53e-01 | 0.1621 |
| 4809 | NHP2L1 | GSM5353225_PA_PR5196-1_Pool_1_2_3_S53_L002 | Human | Prostate | Tumor | 3.27e-04 | 3.87e-01 | 0.1619 |
| 4809 | NHP2L1 | GSM5353226_PA_PR5196-2_Pool_1_2_3_S54_L002 | Human | Prostate | Tumor | 2.91e-04 | 4.64e-01 | 0.159 |
| 4809 | NHP2L1 | GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002 | Human | Prostate | Tumor | 8.34e-05 | 2.62e-01 | 0.1602 |
| 4809 | NHP2L1 | GSM5353232_PA_PR5249_T1_S3_L001 | Human | Prostate | Tumor | 3.03e-02 | 5.21e-01 | 0.1439 |
| 4809 | NHP2L1 | GSM5353236_PA_PR5251_T1_S7_L001 | Human | Prostate | Tumor | 5.78e-05 | 3.68e-01 | 0.1608 |
| 4809 | NHP2L1 | GSM5353237_PA_PR5251_T2_S8_L001 | Human | Prostate | Tumor | 1.03e-11 | 8.03e-01 | 0.1622 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa030408 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
| hsa0304013 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
| hsa0304023 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
| hsa0304033 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
| hsa0304043 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
| hsa0304053 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
| hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030402 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030403 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030404 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa030405 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa030409 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
| hsa0304014 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
| hsa0304024 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
| hsa0304034 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
| hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa030407 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
| hsa0304012 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
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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 |
| Page: 1 |
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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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