Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Gene summary

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Malignant transformation analysis

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Malignant transformation related pathway analysis

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Cell-cell communication analysis

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Single-cell gene regulatory network inference analysis

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Somatic mutation of malignant transformation related genes

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Related drugs of malignant transformation related genes

Gene: HMGA1

Gene summary for HMGA1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

HMGA1

Gene ID

3159

Gene namehigh mobility group AT-hook 1
Gene AliasHMG-R
Cytomap6p21.31
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

P17096


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Malignant transformation analysis

check button 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
check button Malignant transformation involving gene list.
Entrez IDSymbolReplicatesSpeciesOrganTissueAdj P-valueLog2FCMalignancy
3159HMGA1GSM4909281HumanBreastIDC3.28e-031.53e-010.21
3159HMGA1GSM4909285HumanBreastIDC1.05e-102.17e-010.21
3159HMGA1GSM4909286HumanBreastIDC6.39e-20-4.48e-010.1081
3159HMGA1GSM4909288HumanBreastIDC7.24e-06-6.44e-010.0988
3159HMGA1GSM4909293HumanBreastIDC7.37e-18-4.37e-010.1581
3159HMGA1GSM4909294HumanBreastIDC2.82e-13-4.80e-010.2022
3159HMGA1GSM4909296HumanBreastIDC3.18e-16-5.38e-010.1524
3159HMGA1GSM4909297HumanBreastIDC9.90e-29-6.94e-010.1517
3159HMGA1GSM4909298HumanBreastIDC2.77e-23-5.67e-010.1551
3159HMGA1GSM4909299HumanBreastIDC6.96e-22-6.27e-010.035
3159HMGA1GSM4909300HumanBreastIDC1.79e-07-5.95e-010.0334
3159HMGA1GSM4909301HumanBreastIDC4.72e-11-5.29e-010.1577
3159HMGA1GSM4909302HumanBreastIDC4.68e-17-5.94e-010.1545
3159HMGA1GSM4909303HumanBreastIDC1.64e-03-5.56e-010.0438
3159HMGA1GSM4909304HumanBreastIDC9.13e-19-5.73e-010.1636
3159HMGA1GSM4909305HumanBreastIDC1.43e-07-4.67e-010.0436
3159HMGA1GSM4909306HumanBreastIDC1.05e-16-5.03e-010.1564
3159HMGA1GSM4909307HumanBreastIDC3.57e-10-4.10e-010.1569
3159HMGA1GSM4909308HumanBreastIDC9.48e-09-2.95e-010.158
3159HMGA1GSM4909309HumanBreastIDC3.77e-13-5.58e-010.0483
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
BreastThe image shows the 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.IDC: Invasive ductal carcinoma
DCIS: Ductal carcinoma in situ
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Colorectum (GSE201348)The image shows the 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.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The image shows the 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.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
EndometriumThe image shows the 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid Cancer
EsophagusThe image shows the 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.ESCC: Esophageal squamous cell carcinoma
HGIN: High-grade intraepithelial neoplasias
LGIN: Low-grade intraepithelial neoplasias
GCThe image shows the 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.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
LiverThe image shows the 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.HCC: Hepatocellular carcinoma
NAFLD: Non-alcoholic fatty liver disease
Oral CavityThe image shows the 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.EOLP: Erosive Oral lichen planus
LP: leukoplakia
NEOLP: Non-erosive oral lichen planus
OSCC: Oral squamous cell carcinoma
ProstateThe image shows the 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.BPH: Benign Prostatic Hyperplasia
SkinThe image shows the 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.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
ThyroidThe image shows the 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.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

check buttonFind out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
check button Figure of enriched GO biological processes.
TissueDisease StageEnriched GO biological Processes
ColorectumADGO analysis - Figure of enriched GO biological processes: 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).
ColorectumSERGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSSGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSI-HGO analysis - Figure of enriched GO biological processes: 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).
ColorectumFAPGO analysis - Figure of enriched GO biological processes: 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).
∗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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check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:00075688BreastPrecanceraging41/1080339/187235.95e-061.71e-0441
GO:00224119BreastPrecancercellular component disassembly44/1080443/187233.17e-044.51e-0344
GO:00329865BreastPrecancerprotein-DNA complex disassembly6/108020/187236.99e-048.43e-036
GO:00075694BreastPrecancercell aging17/1080132/187231.55e-031.59e-0217
GO:00903423BreastPrecancerregulation of cell aging10/108061/187232.40e-032.21e-0210
GO:000756813BreastIDCaging52/1434339/187231.14e-065.10e-0552
GO:00096157BreastIDCresponse to virus47/1434367/187233.53e-045.16e-0347
GO:003298612BreastIDCprotein-DNA complex disassembly6/143420/187233.03e-032.60e-026
GO:000756912BreastIDCcell aging19/1434132/187235.63e-034.08e-0219
GO:00903421BreastIDCregulation of cell aging11/143461/187236.10e-034.36e-0211
GO:000756823BreastDCISaging50/1390339/187232.38e-068.46e-0550
GO:000961512BreastDCISresponse to virus45/1390367/187236.16e-047.82e-0345
GO:003298621BreastDCISprotein-DNA complex disassembly6/139020/187232.59e-032.30e-026
GO:000756921BreastDCIScell aging19/1390132/187234.03e-033.20e-0219
GO:00903422BreastDCISregulation of cell aging11/139061/187234.84e-033.67e-0211
GO:002241113BreastDCIScellular component disassembly48/1390443/187235.35e-033.92e-0248
GO:0022411ColorectumADcellular component disassembly147/3918443/187238.53e-106.76e-08147
GO:0032984ColorectumADprotein-containing complex disassembly81/3918224/187239.41e-084.65e-0681
GO:0006325ColorectumADchromatin organization119/3918409/187234.85e-058.33e-04119
GO:0032986ColorectumADprotein-DNA complex disassembly12/391820/187231.60e-042.21e-0312
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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Cell-cell communication analysis

check buttonIdentification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states
LigandReceptorLRpairPathwayTissueDisease Stage
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Single-cell gene regulatory network inference analysis

check buttonFind out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
TFCell TypeTissueDisease StageTarget GeneRSSRegulon Activity
HMGA1TH17ColorectumADJMYBL2,HMGN1,MARCKSL1, etc.8.23e-02The 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.
HMGA1CD8TEXINTColorectumADJMYBL2,HMGN1,MARCKSL1, etc.1.21e-01The 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.
HMGA1CD8TEXPColorectumADJMYBL2,HMGN1,MARCKSL1, etc.5.77e-02The 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.
HMGA1CD8TEXPColorectumMSSMYBL2,HMGN1,MARCKSL1, etc.1.98e-01The 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.
HMGA1ABPLungHealthySMC2,HSPB1,ZWINT, etc.9.10e-02The 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.
HMGA1GDTOral cavityNEOLPLIMD2,RPS18,RPL27A, etc.1.85e-01The 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.
HMGA1CD8TEXINTOral cavityNEOLPLIMD2,RPS18,RPL27A, etc.1.67e-01The 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.
HMGA1TH17Oral cavityNEOLPLIMD2,RPS18,RPL27A, etc.4.37e-02The 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.
HMGA1DUCT2PancreasHealthyCLDND1,IFNGR2,NCEH1, etc.9.54e-02The 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.
HMGA1pDCProstateHealthyS100A6,S100A14,PDLIM4, etc.2.05e-01The 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.
∗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

check buttonAnnotation of somatic variants for genes involved in malignant transformation
Hugo SymbolVariant ClassVariant ClassificationdbSNP RSHGVScHGVSpHGVSp ShortSWISSPROTBIOTYPESIFTPolyPhenTumor Sample BarcodeTissueHistologySexAgeStageTherapy TypesDrugsOutcome
HMGA1SNVMissense_Mutationc.165N>Cp.Lys55Asnp.K55NP17096protein_codingdeleterious(0)benign(0)TCGA-Q1-A73P-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
HMGA1SNVMissense_Mutationc.118N>Ap.Ala40Thrp.A40TP17096protein_codingtolerated_low_confidence(0.33)benign(0.036)TCGA-AD-5900-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
HMGA1SNVMissense_Mutationc.172C>Tp.Arg58Trpp.R58WP17096protein_codingtolerated(0.09)possibly_damaging(0.898)TCGA-CG-4306-01Stomachstomach adenocarcinomaMale>=65III/IVUnknownUnknownSD
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Related drugs of malignant transformation related genes

check buttonIdentification of chemicals and drugs interact with genes involved in malignant transfromation
(DGIdb 4.0)
Entrez IDSymbolCategoryInteraction TypesDrug Claim NameDrug NamePMIDs
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