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Gene: HCLS1 |
Gene summary for HCLS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HCLS1 | Gene ID | 3059 |
| Gene name | hematopoietic cell-specific Lyn substrate 1 | |
| Gene Alias | CTTNL | |
| Cytomap | 3q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | P14317 |
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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 |
| 3059 | HCLS1 | LZE2D | Human | Esophagus | HGIN | 8.75e-03 | 5.55e-01 | 0.0642 |
| 3059 | HCLS1 | LZE4T | Human | Esophagus | ESCC | 4.80e-07 | 3.15e-01 | 0.0811 |
| 3059 | HCLS1 | LZE5T | Human | Esophagus | ESCC | 4.96e-05 | 3.33e-01 | 0.0514 |
| 3059 | HCLS1 | LZE7T | Human | Esophagus | ESCC | 5.99e-08 | 5.06e-01 | 0.0667 |
| 3059 | HCLS1 | LZE22D1 | Human | Esophagus | HGIN | 9.40e-04 | 2.26e-01 | 0.0595 |
| 3059 | HCLS1 | LZE22T | Human | Esophagus | ESCC | 9.86e-05 | 3.85e-01 | 0.068 |
| 3059 | HCLS1 | LZE24T | Human | Esophagus | ESCC | 1.95e-02 | 1.13e-01 | 0.0596 |
| 3059 | HCLS1 | LZE6T | Human | Esophagus | ESCC | 8.68e-15 | 6.67e-01 | 0.0845 |
| 3059 | HCLS1 | P1T-E | Human | Esophagus | ESCC | 5.07e-05 | 5.41e-01 | 0.0875 |
| 3059 | HCLS1 | P8T-E | Human | Esophagus | ESCC | 3.32e-61 | 1.06e+00 | 0.0889 |
| 3059 | HCLS1 | P15T-E | Human | Esophagus | ESCC | 6.11e-27 | 6.88e-01 | 0.1149 |
| 3059 | HCLS1 | P23T-E | Human | Esophagus | ESCC | 1.07e-28 | 8.90e-01 | 0.108 |
| 3059 | HCLS1 | P28T-E | Human | Esophagus | ESCC | 3.87e-03 | 2.09e-01 | 0.1149 |
| 3059 | HCLS1 | P47T-E | Human | Esophagus | ESCC | 3.86e-17 | 4.29e-01 | 0.1067 |
| 3059 | HCLS1 | P61T-E | Human | Esophagus | ESCC | 2.24e-34 | 9.22e-01 | 0.099 |
| 3059 | HCLS1 | P65T-E | Human | Esophagus | ESCC | 7.25e-03 | 1.40e-01 | 0.0978 |
| 3059 | HCLS1 | P74T-E | Human | Esophagus | ESCC | 1.25e-02 | 1.80e-01 | 0.1479 |
| 3059 | HCLS1 | P76T-E | Human | Esophagus | ESCC | 1.72e-04 | 2.19e-01 | 0.1207 |
| 3059 | HCLS1 | P127T-E | Human | Esophagus | ESCC | 2.66e-41 | 8.47e-01 | 0.0826 |
| 3059 | HCLS1 | P128T-E | Human | Esophagus | ESCC | 3.39e-38 | 1.40e+00 | 0.1241 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:007259420 | Esophagus | HGIN | establishment of protein localization to organelle | 120/2587 | 422/18723 | 1.73e-15 | 4.00e-13 | 120 |
| GO:003450417 | Esophagus | HGIN | protein localization to nucleus | 84/2587 | 290/18723 | 1.06e-11 | 1.24e-09 | 84 |
| GO:000691319 | Esophagus | HGIN | nucleocytoplasmic transport | 83/2587 | 301/18723 | 2.14e-10 | 1.97e-08 | 83 |
| GO:005116919 | Esophagus | HGIN | nuclear transport | 83/2587 | 301/18723 | 2.14e-10 | 1.97e-08 | 83 |
| GO:190382926 | Esophagus | HGIN | positive regulation of cellular protein localization | 75/2587 | 276/18723 | 3.19e-09 | 2.30e-07 | 75 |
| GO:004682219 | Esophagus | HGIN | regulation of nucleocytoplasmic transport | 35/2587 | 106/18723 | 3.69e-07 | 1.69e-05 | 35 |
| GO:190018216 | Esophagus | HGIN | positive regulation of protein localization to nucleus | 30/2587 | 87/18723 | 8.74e-07 | 3.59e-05 | 30 |
| GO:003238617 | Esophagus | HGIN | regulation of intracellular transport | 79/2587 | 337/18723 | 1.11e-06 | 4.36e-05 | 79 |
| GO:190018017 | Esophagus | HGIN | regulation of protein localization to nucleus | 40/2587 | 136/18723 | 1.69e-06 | 6.31e-05 | 40 |
| GO:003315720 | Esophagus | HGIN | regulation of intracellular protein transport | 58/2587 | 229/18723 | 2.29e-06 | 8.29e-05 | 58 |
| GO:004325427 | Esophagus | HGIN | regulation of protein-containing complex assembly | 94/2587 | 428/18723 | 2.39e-06 | 8.55e-05 | 94 |
| GO:004682416 | Esophagus | HGIN | positive regulation of nucleocytoplasmic transport | 23/2587 | 62/18723 | 3.94e-06 | 1.32e-04 | 23 |
| GO:190495120 | Esophagus | HGIN | positive regulation of establishment of protein localization | 73/2587 | 319/18723 | 6.99e-06 | 2.14e-04 | 73 |
| GO:003238820 | Esophagus | HGIN | positive regulation of intracellular transport | 51/2587 | 202/18723 | 1.00e-05 | 2.92e-04 | 51 |
| GO:003009927 | Esophagus | HGIN | myeloid cell differentiation | 83/2587 | 381/18723 | 1.26e-05 | 3.52e-04 | 83 |
| GO:001703817 | Esophagus | HGIN | protein import | 51/2587 | 206/18723 | 1.79e-05 | 4.86e-04 | 51 |
| GO:009031616 | Esophagus | HGIN | positive regulation of intracellular protein transport | 42/2587 | 160/18723 | 2.18e-05 | 5.78e-04 | 42 |
| GO:005117010 | Esophagus | HGIN | import into nucleus | 41/2587 | 159/18723 | 4.24e-05 | 1.04e-03 | 41 |
| GO:005125826 | Esophagus | HGIN | protein polymerization | 66/2587 | 297/18723 | 4.96e-05 | 1.19e-03 | 66 |
| GO:005122220 | Esophagus | HGIN | positive regulation of protein transport | 67/2587 | 303/18723 | 5.13e-05 | 1.22e-03 | 67 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513139 | Esophagus | HGIN | Shigellosis | 71/1383 | 247/8465 | 4.89e-07 | 7.98e-06 | 6.34e-06 | 71 |
| hsa0510039 | Esophagus | HGIN | Bacterial invasion of epithelial cells | 30/1383 | 77/8465 | 1.49e-06 | 2.31e-05 | 1.84e-05 | 30 |
| hsa0513039 | Esophagus | HGIN | Pathogenic Escherichia coli infection | 54/1383 | 197/8465 | 4.91e-05 | 6.15e-04 | 4.89e-04 | 54 |
| hsa0453039 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
| hsa0520528 | Esophagus | HGIN | Proteoglycans in cancer | 47/1383 | 205/8465 | 8.23e-03 | 4.71e-02 | 3.74e-02 | 47 |
| hsa05131114 | Esophagus | HGIN | Shigellosis | 71/1383 | 247/8465 | 4.89e-07 | 7.98e-06 | 6.34e-06 | 71 |
| hsa05100114 | Esophagus | HGIN | Bacterial invasion of epithelial cells | 30/1383 | 77/8465 | 1.49e-06 | 2.31e-05 | 1.84e-05 | 30 |
| hsa05130115 | Esophagus | HGIN | Pathogenic Escherichia coli infection | 54/1383 | 197/8465 | 4.91e-05 | 6.15e-04 | 4.89e-04 | 54 |
| hsa04530115 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
| hsa05205112 | Esophagus | HGIN | Proteoglycans in cancer | 47/1383 | 205/8465 | 8.23e-03 | 4.71e-02 | 3.74e-02 | 47 |
| hsa05131211 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa05130211 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
| hsa0520529 | Esophagus | ESCC | Proteoglycans in cancer | 138/4205 | 205/8465 | 1.79e-07 | 1.40e-06 | 7.15e-07 | 138 |
| hsa05100211 | Esophagus | ESCC | Bacterial invasion of epithelial cells | 59/4205 | 77/8465 | 1.05e-06 | 6.76e-06 | 3.46e-06 | 59 |
| hsa04530211 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa05131310 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa05130310 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
| hsa0520537 | Esophagus | ESCC | Proteoglycans in cancer | 138/4205 | 205/8465 | 1.79e-07 | 1.40e-06 | 7.15e-07 | 138 |
| hsa05100310 | Esophagus | ESCC | Bacterial invasion of epithelial cells | 59/4205 | 77/8465 | 1.05e-06 | 6.76e-06 | 3.46e-06 | 59 |
| hsa04530310 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| Page: 1 2 3 |
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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 |
| HCLS1 | M2MAC | Esophagus | ADJ | FUBP1,HEXB,FENDRR, etc. | 2.84e-01 |  |
| HCLS1 | M2MAC | Esophagus | ESCC | FUBP1,HEXB,FENDRR, etc. | 2.94e-01 |  |
| ∗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 |
| HCLS1 | SNV | Missense_Mutation | novel | c.495N>C | p.Lys165Asn | p.K165N | P14317 | protein_coding | deleterious(0.01) | possibly_damaging(0.88) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
| HCLS1 | SNV | Missense_Mutation | rs202020296 | c.631N>A | p.Gly211Ser | p.G211S | P14317 | protein_coding | tolerated(0.13) | possibly_damaging(0.596) | TCGA-AC-A8OP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| HCLS1 | SNV | Missense_Mutation | c.304N>C | p.Glu102Gln | p.E102Q | P14317 | protein_coding | deleterious(0) | probably_damaging(0.949) | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| HCLS1 | SNV | Missense_Mutation | c.158N>C | p.Asn53Thr | p.N53T | P14317 | protein_coding | deleterious(0) | benign(0.283) | TCGA-EK-A2RN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| HCLS1 | SNV | Missense_Mutation | rs767550556 | c.553G>A | p.Glu185Lys | p.E185K | P14317 | protein_coding | deleterious(0.01) | probably_damaging(0.917) | TCGA-AA-3511-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| HCLS1 | SNV | Missense_Mutation | rs147125943 | c.1300N>A | p.Val434Met | p.V434M | P14317 | protein_coding | deleterious(0.05) | possibly_damaging(0.622) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| HCLS1 | SNV | Missense_Mutation | rs770634522 | c.278N>A | p.Arg93Gln | p.R93Q | P14317 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| HCLS1 | SNV | Missense_Mutation | c.114N>T | p.Trp38Cys | p.W38C | P14317 | protein_coding | deleterious(0) | benign(0.185) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HCLS1 | SNV | Missense_Mutation | novel | c.824N>A | p.Ser275Asn | p.S275N | P14317 | protein_coding | tolerated(0.55) | benign(0.09) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| HCLS1 | SNV | Missense_Mutation | c.1415N>A | p.Gly472Asp | p.G472D | P14317 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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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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