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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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: HAP1

Gene summary for HAP1

Gene summary.

Gene information	Species	Human
	Gene symbol	HAP1
	Gene ID	9001
	Gene name	huntingtin associated protein 1
	Gene Alias	HAP2
	Cytomap	17q21.2
	Gene Type	protein-coding
	GO ID	GO:0006518
	UniProtAcc	P54257

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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
9001	HAP1	LZE4T	Human	Esophagus	ESCC	7.80e-18	5.94e-01	0.0811
9001	HAP1	LZE7T	Human	Esophagus	ESCC	1.30e-02	2.00e-01	0.0667
9001	HAP1	LZE21D1	Human	Esophagus	HGIN	2.44e-05	5.01e-01	0.0632
9001	HAP1	LZE21T	Human	Esophagus	ESCC	3.39e-07	4.56e-01	0.0655
9001	HAP1	P1T-E	Human	Esophagus	ESCC	1.22e-11	6.70e-01	0.0875
9001	HAP1	P4T-E	Human	Esophagus	ESCC	1.03e-21	5.20e-01	0.1323
9001	HAP1	P5T-E	Human	Esophagus	ESCC	3.89e-12	3.06e-01	0.1327
9001	HAP1	P8T-E	Human	Esophagus	ESCC	1.78e-03	1.15e-01	0.0889
9001	HAP1	P9T-E	Human	Esophagus	ESCC	1.06e-16	4.00e-01	0.1131
9001	HAP1	P10T-E	Human	Esophagus	ESCC	6.62e-20	3.41e-01	0.116
9001	HAP1	P11T-E	Human	Esophagus	ESCC	4.48e-08	5.13e-01	0.1426
9001	HAP1	P12T-E	Human	Esophagus	ESCC	6.31e-48	8.25e-01	0.1122
9001	HAP1	P15T-E	Human	Esophagus	ESCC	6.86e-44	9.34e-01	0.1149
9001	HAP1	P16T-E	Human	Esophagus	ESCC	7.90e-03	1.16e-01	0.1153
9001	HAP1	P20T-E	Human	Esophagus	ESCC	6.70e-05	2.07e-01	0.1124
9001	HAP1	P22T-E	Human	Esophagus	ESCC	4.09e-46	9.18e-01	0.1236
9001	HAP1	P24T-E	Human	Esophagus	ESCC	9.20e-06	2.22e-01	0.1287
9001	HAP1	P26T-E	Human	Esophagus	ESCC	3.60e-13	2.74e-01	0.1276
9001	HAP1	P27T-E	Human	Esophagus	ESCC	2.06e-08	3.23e-01	0.1055
9001	HAP1	P28T-E	Human	Esophagus	ESCC	1.77e-22	5.10e-01	0.1149

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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

∗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:000660525	Esophagus	HGIN	protein targeting	78/2587	314/18723	1.08e-07	5.47e-06	78
GO:005165616	Esophagus	HGIN	establishment of organelle localization	90/2587	390/18723	4.27e-07	1.94e-05	90
GO:003238617	Esophagus	HGIN	regulation of intracellular transport	79/2587	337/18723	1.11e-06	4.36e-05	79
GO:00342496	Esophagus	HGIN	negative regulation of cellular amide metabolic process	66/2587	273/18723	2.74e-06	9.60e-05	66
GO:005165126	Esophagus	HGIN	maintenance of location in cell	53/2587	214/18723	1.22e-05	3.45e-04	53
GO:005123520	Esophagus	HGIN	maintenance of location	73/2587	327/18723	1.73e-05	4.71e-04	73
GO:19021156	Esophagus	HGIN	regulation of organelle assembly	46/2587	186/18723	4.63e-05	1.12e-03	46
GO:003070517	Esophagus	HGIN	cytoskeleton-dependent intracellular transport	45/2587	195/18723	3.07e-04	5.15e-03	45
GO:19028552	Esophagus	HGIN	regulation of non-motile cilium assembly	6/2587	10/18723	8.81e-04	1.13e-02	6
GO:003812717	Esophagus	HGIN	ERBB signaling pathway	29/2587	121/18723	1.83e-03	1.97e-02	29
GO:00109707	Esophagus	HGIN	transport along microtubule	35/2587	155/18723	2.01e-03	2.12e-02	35
GO:005165010	Esophagus	HGIN	establishment of vesicle localization	35/2587	161/18723	3.89e-03	3.54e-02	35
GO:00516542	Esophagus	HGIN	establishment of mitochondrion localization	10/2587	29/18723	4.07e-03	3.65e-02	10
GO:19011848	Esophagus	HGIN	regulation of ERBB signaling pathway	20/2587	79/18723	4.56e-03	3.96e-02	20
GO:006049117	Esophagus	HGIN	regulation of cell projection assembly	39/2587	188/18723	5.61e-03	4.57e-02	39
GO:000717317	Esophagus	HGIN	epidermal growth factor receptor signaling pathway	25/2587	108/18723	5.87e-03	4.77e-02	25
GO:005164810	Esophagus	HGIN	vesicle localization	37/2587	177/18723	6.03e-03	4.87e-02	37
GO:00346432	Esophagus	HGIN	establishment of mitochondrion localization, microtubule-mediated	9/2587	26/18723	6.15e-03	4.92e-02	9
GO:00474972	Esophagus	HGIN	mitochondrion transport along microtubule	9/2587	26/18723	6.15e-03	4.92e-02	9
GO:003238618	Esophagus	ESCC	regulation of intracellular transport	243/8552	337/18723	3.20e-23	7.25e-21	243

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501630	Esophagus	HGIN	Huntington disease	129/1383	306/8465	6.81e-28	7.41e-26	5.88e-26	129
hsa0501430	Esophagus	HGIN	Amyotrophic lateral sclerosis	140/1383	364/8465	2.13e-25	1.16e-23	9.19e-24	140
hsa0502230	Esophagus	HGIN	Pathways of neurodegeneration - multiple diseases	153/1383	476/8465	1.22e-18	4.41e-17	3.50e-17	153
hsa05016113	Esophagus	HGIN	Huntington disease	129/1383	306/8465	6.81e-28	7.41e-26	5.88e-26	129
hsa05014113	Esophagus	HGIN	Amyotrophic lateral sclerosis	140/1383	364/8465	2.13e-25	1.16e-23	9.19e-24	140
hsa05022113	Esophagus	HGIN	Pathways of neurodegeneration - multiple diseases	153/1383	476/8465	1.22e-18	4.41e-17	3.50e-17	153
hsa05014210	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa05016210	Esophagus	ESCC	Huntington disease	226/4205	306/8465	1.38e-18	8.72e-17	4.46e-17	226
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
hsa0501638	Esophagus	ESCC	Huntington disease	226/4205	306/8465	1.38e-18	8.72e-17	4.46e-17	226
hsa0502238	Esophagus	ESCC	Pathways of neurodegeneration - multiple diseases	318/4205	476/8465	6.10e-15	2.04e-13	1.05e-13	318
hsa0501428	Oral cavity	OSCC	Amyotrophic lateral sclerosis	246/3704	364/8465	6.65e-21	1.11e-18	5.67e-19	246
hsa0501628	Oral cavity	OSCC	Huntington disease	204/3704	306/8465	1.70e-16	7.13e-15	3.63e-15	204
hsa0502228	Oral cavity	OSCC	Pathways of neurodegeneration - multiple diseases	292/3704	476/8465	1.60e-15	4.47e-14	2.28e-14	292
hsa05014112	Oral cavity	OSCC	Amyotrophic lateral sclerosis	246/3704	364/8465	6.65e-21	1.11e-18	5.67e-19	246
hsa05016112	Oral cavity	OSCC	Huntington disease	204/3704	306/8465	1.70e-16	7.13e-15	3.63e-15	204
hsa05022112	Oral cavity	OSCC	Pathways of neurodegeneration - multiple diseases	292/3704	476/8465	1.60e-15	4.47e-14	2.28e-14	292
hsa0501429	Oral cavity	LP	Amyotrophic lateral sclerosis	197/2418	364/8465	1.25e-25	1.39e-23	8.93e-24	197
hsa0501629	Oral cavity	LP	Huntington disease	172/2418	306/8465	6.31e-25	5.25e-23	3.39e-23	172

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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

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

HAP1

SNV

Missense_Mutation

rs782546957

c.1301N>T

p.Thr434Met

p.T434M

P54257

protein_coding

deleterious(0.02)

probably_damaging(0.951)

TCGA-A7-A425-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

adriamycin

HAP1

SNV

Missense_Mutation

novel

c.1307C>A

p.Ala436Asp

p.A436D

P54257

protein_coding

tolerated(0.06)

probably_damaging(0.997)

TCGA-AC-A8OP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HAP1

SNV

Missense_Mutation

c.1030G>A

p.Glu344Lys

p.E344K

P54257

protein_coding

tolerated(0.25)

benign(0.048)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

HAP1

SNV

Missense_Mutation

rs782311151

c.1825N>A

p.Ala609Thr

p.A609T

P54257

protein_coding

tolerated_low_confidence(0.08)

benign(0.02)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

HAP1

SNV

Missense_Mutation

novel

c.1312N>A

p.Glu438Lys

p.E438K

P54257

protein_coding

deleterious(0.04)

probably_damaging(0.987)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

HAP1

SNV

Missense_Mutation

c.1630N>A

p.Glu544Lys

p.E544K

P54257

protein_coding

deleterious(0)

benign(0.225)

TCGA-C5-A1MK-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

carboplatin

HAP1

SNV

Missense_Mutation

c.1147G>A

p.Glu383Lys

p.E383K

P54257

protein_coding

deleterious(0.01)

possibly_damaging(0.882)

TCGA-EK-A2R8-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

HAP1

SNV

Missense_Mutation

c.185C>T

p.Ser62Leu

p.S62L

P54257

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.572)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

HAP1

SNV

Missense_Mutation

c.955G>A

p.Glu319Lys

p.E319K

P54257

protein_coding

tolerated(0.33)

benign(0.013)

TCGA-LP-A5U2-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

HAP1

SNV

Missense_Mutation

rs555784831

c.1630N>C

p.Glu544Gln

p.E544Q

P54257

protein_coding

deleterious(0)

possibly_damaging(0.891)

TCGA-VS-A9U7-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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