Cancer CRCdb

TF information

TF name:	ATF4
TF family:	TF_bZIP
Ensembl gene ID:	ENSG00000128272
Ensembl protein ID:	ENSP00000336790, ENSP00000384587, ENSP00000379912
Entrez gene ID:	468

Database name	Link	Database name	Link
NCBI Gene:		Genecards:
Uniprot:		Wikipedia:
Cosmic 3D:		Geneontology:
CCLE:

Frequency of ATF4 in all biosamples

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Sample ID	Biosample type	Tissue type	Biosample name	TF Frequency
Sample_02_242	Cell line	Colon	V481	0.19089277703006
Sample_02_296	Cell line	Neuroblastoma	CLB-BER-Lud	0.08645753634277
Sample_02_299	Cell line	Neuroblastoma	CLB-MA	0.29016786570743
Sample_02_304	Cell line	Neuroblastoma	N206	0.1195652173913
Sample_02_355	Cell line	Colon	HCT15	0.10714285714286

ATF4 distribution in samples’ most representative CRC

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Sample ID	Tissue type	Biosample type	Biosample name

ATF4 distribution in all CRCs

Genomic distribution of SEs associated with ATF4

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Mutation of ATF4

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Database name	Link
gnomAD:	gnomAD
ExAC:	ExAC
ICGC:

Database name	Link
Cosmic:
Cosmic cell lines:
Depmap:

TCGA somatic mutations and clinical variants of ATF4

rsID	Chr	Start	Stop	Ref	Alt	Gene_region	Gene_symble	Effect	TCGA_Occurrence
rs1803323	chr22	39918323	39918323	C	G	exonic	ATF4	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr22	39918236	39918236	C	A	exonic	ATF4	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr22	39917506	39917506	C	T	exonic	ATF4	nonsynonymous	LIHC\|1\|373\|0.00268,SKCM\|1\|368\|0.00272
-	chr22	39917554	39917554	A	C	exonic	ATF4	nonsynonymous	CHOL\|1\|35\|0.02857
-	chr22	39917987	39917987	G	T	exonic	ATF4	stopgain	GBMLGG\|1\|820\|0.00122,LGG\|1\|530\|0.00189
rs148038848	chr22	39917610	39917610	G	A	exonic	ATF4	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr22	39917510	39917510	C	T	exonic	ATF4	synonymous	CESC\|1\|194\|0.00515,ESCA\|1\|185\|0.00541
-	chr22	39917911	39917912	TG	-	exonic	ATF4	frameshift	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222
-	chr22	39917510	39917510	C	G	exonic	ATF4	nonsynonymous	BRCA\|1\|982\|0.00102
-	chr22	39917600	39917600	C	T	exonic	ATF4	synonymous	SKCM\|1\|368\|0.00272
-	chr22	39918324	39918324	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39917511	39917511	G	C	exonic	ATF4	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr22	39917628	39917628	G	A	exonic	ATF4	nonsynonymous	BLCA\|1\|396\|0.00253
rs767181464	chr22	39917917	39917917	C	G	exonic	ATF4	synonymous	HNSC\|1\|512\|0.00195
rs34854854	chr22	39917503	39917503	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39918017	39918017	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39918485	39918485	G	C	exonic	ATF4	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr22	39918267	39918267	G	-	exonic	ATF4	frameshift	LIHC\|1\|373\|0.00268
-	chr22	39918080	39918082	TCC	-	exonic	ATF4	nonframeshift	BRCA\|1\|982\|0.00102
-	chr22	39918059	39918059	C	A	exonic	ATF4	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr22	39917980	39917980	T	A	exonic	ATF4	nonsynonymous	LUSC\|1\|178\|0.00562
-	chr22	39918445	39918445	G	A	exonic	ATF4	synonymous	BLCA\|1\|396\|0.00253
-	chr22	39917489	39917489	G	-	exonic	ATF4	frameshift	LIHC\|1\|373\|0.00268
-	chr22	39917951	39917951	C	-	exonic	ATF4	frameshift	PAAD\|1\|185\|0.00541,PRAD\|1\|499\|0.00200,STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs770192882	chr22	39917950	39917950	-	C	exonic	ATF4	frameshift	BRCA\|1\|982\|0.00102,KIPAN\|7\|799\|0.00876,KIRC\|7\|451\|0.01552,PAAD\|1\|185\|0.00541,STAD\|2\|395\|0.00506,STES\|2\|395\|0.00506
-	chr22	39918168	39918168	A	G	exonic	ATF4	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr22	39918398	39918398	A	-	exonic	ATF4	frameshift	COADREAD\|2\|489\|0.00409,READ\|2\|122\|0.01639
-	chr22	39917519	39917519	G	C	exonic	ATF4	synonymous	HNSC\|1\|512\|0.00195
rs757102478	chr22	39918231	39918231	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39917809	39917809	G	A	exonic	ATF4	synonymous	CESC\|1\|194\|0.00515
-	chr22	39917879	39917879	G	A	exonic	ATF4	nonsynonymous	HNSC\|1\|512\|0.00195
rs779679328	chr22	39918018	39918018	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39918415	39918415	C	G	exonic	ATF4	nonsynonymous	ESCA\|1\|185\|0.00541
rs200926784	chr22	39917543	39917543	A	G	exonic	ATF4	synonymous	PRAD\|1\|499\|0.00200
-	chr22	39918129	39918129	G	A	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39918557	39918557	G	T	exonic	ATF4	nonsynonymous	BLCA\|1\|396\|0.00253
-	chr22	39917981	39917981	C	G	exonic	ATF4	nonsynonymous	CESC\|1\|194\|0.00515
rs547982920	chr22	39918236	39918236	C	G	exonic	ATF4	nonsynonymous	CESC\|1\|194\|0.00515
-	chr22	39918282	39918282	G	T	exonic	ATF4	nonsynonymous	COADREAD\|1\|489\|0.00204,READ\|1\|122\|0.00820
-	chr22	39917856	39917856	T	C	exonic	ATF4	nonsynonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr22	39917549	39917549	C	G	exonic	ATF4	synonymous	CESC\|2\|194\|0.01031
rs539627686	chr22	39918189	39918189	C	T	exonic	ATF4	nonsynonymous	ACC\|1\|90\|0.01111
-	chr22	39917837	39917837	T	C	exonic	ATF4	synonymous	BRCA\|1\|982\|0.00102
rs146204295	chr22	39918130	39918130	G	A	exonic	ATF4	synonymous	SKCM\|1\|368\|0.00272
-	chr22	39917608	39917608	-	G	exonic	ATF4	frameshift	ESCA\|1\|185\|0.00541
rs375843215	chr22	39917561	39917561	C	T	exonic	ATF4	synonymous	DLBC\|1\|48\|0.02083
rs141575018	chr22	39917787	39917787	T	G	exonic	ATF4	nonsynonymous	DLBC\|1\|48\|0.02083
-	chr22	39918182	39918182	G	A	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39917932	39917932	C	G	exonic	ATF4	synonymous	LUSC\|1\|178\|0.00562
-	chr22	39918195	39918195	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39917485	39917485	T	C	exonic	ATF4	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr22	39918330	39918330	C	T	exonic	ATF4	nonsynonymous	SKCM\|1\|368\|0.00272
-	chr22	39918248	39918248	C	G	exonic	ATF4	nonsynonymous	BRCA\|1\|982\|0.00102
rs777087053	chr22	39918553	39918553	G	A	exonic	ATF4	synonymous	BLCA\|1\|396\|0.00253
-	chr22	39918064	39918064	C	A	exonic	ATF4	synonymous	SKCM\|1\|368\|0.00272
rs754079438	chr22	39917859	39917859	A	G	exonic	ATF4	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr22	39918604	39918604	C	A	exonic	ATF4	synonymous	HNSC\|1\|512\|0.00195
-	chr22	39918110	39918110	G	A	exonic	ATF4	nonsynonymous	HNSC\|1\|512\|0.00195
-	chr22	39918438	39918438	G	A	exonic	ATF4	nonsynonymous	STAD\|1\|395\|0.00253,STES\|1\|395\|0.00253
rs372679887	chr22	39918368	39918368	G	A	exonic	ATF4	nonsynonymous	LIHC\|1\|373\|0.00268
-	chr22	39918463	39918463	G	T	exonic	ATF4	nonsynonymous	UCEC\|1\|248\|0.00403
-	chr22	39917546	39917546	T	G	exonic	ATF4	synonymous	SARC\|1\|247\|0.00405
rs781776700	chr22	39917992	39917992	T	C	exonic	ATF4	synonymous	COAD\|1\|367\|0.00272,COADREAD\|1\|489\|0.00204
-	chr22	39917589	39917589	C	T	exonic	ATF4	nonsynonymous	LUAD\|1\|543\|0.00184
-	chr22	39917471	39917471	G	C	exonic	ATF4	synonymous	BLCA\|1\|396\|0.00253
-	chr22	39918544	39918544	C	A	exonic	ATF4	synonymous	KIPAN\|1\|799\|0.00125,KIRP\|1\|282\|0.00355
-	chr22	39917921	39917921	-	C	exonic	ATF4	frameshift	KIPAN\|1\|799\|0.00125,KIRC\|1\|451\|0.00222,LUAD\|1\|543\|0.00184
-	chr22	39917481	39917481	G	C	exonic	ATF4	nonsynonymous	LUSC\|1\|178\|0.00562

Disease information of ATF4

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TF_name	Disease_name	Disease_class	Disease_semantic_type	TF_disease_source
ATF4	Anoxemia	C23	Sign or Symptom	CTD_human
ATF4	Anoxia	C23	Pathologic Function	CTD_human
ATF4	Bipolar Disorder	F03	Mental or Behavioral Dysfunction	PSYGENET
ATF4	Mental Depression	F01	Mental or Behavioral Dysfunction	PSYGENET
ATF4	Depressive disorder	F03	Mental or Behavioral Dysfunction	PSYGENET
ATF4	Fatty Liver	C06	Disease or Syndrome	CTD_human
ATF4	Mammary Ductal Carcinoma	C04;C17	Neoplastic Process	CTD_human
ATF4	Necrosis	C23	Organ or Tissue Function	CTD_human
ATF4	Schizophrenia	F03	Mental or Behavioral Dysfunction	PSYGENET
ATF4	Hypoxia	C23	Pathologic Function	CTD_human
ATF4	Hypoxemia	C23	Finding	CTD_human
ATF4	Invasive Ductal Breast Carcinoma	C04;C17	Neoplastic Process	CTD_human
ATF4	Steatohepatitis	C06	Disease or Syndrome	CTD_human

Pathway associated with ATF4

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pathway_ID	pathway_name	pathway_source	gene_number	edge_number
pathway0000196	Apoptosis signaling pathway	panther	104	1308
pathway0000230	ATF4 activates genes	reactome	25	112
pathway0000231	ATF6-alpha activates chaperone genes	reactome	10	27
pathway0002392	Validated transcriptional targets of AP1 family members Fra1 and Fra2	pid	37	165
pathway0002743	Hs_VEGFA-VEGFR2_Signaling_Pathway_WP3888_90000	wikipathways	153	1949
pathway0002755	Hs_White_fat_cell_differentiation_WP3946_90940	wikipathways	30	59
pathway0002817	Hs_One_Carbon_Metabolism_WP241_89671	wikipathways	14	29

Go term information of ATF4

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GO_term_name	GO_term_type	TF_name
GO_REGULATION_OF_TRANSLATION_IN_RESPONSE_TO_STRESS	BP	ATF4
GO_CELLULAR_RESPONSE_TO_UV	BP	ATF4
GO_CELLULAR_RESPONSE_TO_LIGHT_STIMULUS	BP	ATF4
GO_CELLULAR_RESPONSE_TO_EXTRACELLULAR_STIMULUS	BP	ATF4
GO_GAMMA_AMINOBUTYRIC_ACID_SIGNALING_PATHWAY	BP	ATF4
GO_NEGATIVE_REGULATION_OF_RESPONSE_TO_OXIDATIVE_STRESS	BP	ATF4
GO_NEGATIVE_REGULATION_OF_CELLULAR_AMIDE_METABOLIC_PROCESS	BP	ATF4
GO_NEGATIVE_REGULATION_OF_TRANSLATIONAL_INITIATION	BP	ATF4
GO_RESPONSE_TO_METAL_ION	BP	ATF4
GO_NEGATIVE_REGULATION_OF_POTASSIUM_ION_TRANSPORT	BP	ATF4
GO_ER_NUCLEUS_SIGNALING_PATHWAY	BP	ATF4
GO_REGULATION_OF_METAL_ION_TRANSPORT	BP	ATF4
GO_MONOSACCHARIDE_BIOSYNTHETIC_PROCESS	BP	ATF4
GO_CELLULAR_RESPONSE_TO_ARSENIC_CONTAINING_SUBSTANCE	BP	ATF4
GO_POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER_IN_RESPONSE_TO_STRESS	BP	ATF4
GO_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_I_PROMOTER	BP	ATF4
GO_CARBOHYDRATE_BIOSYNTHETIC_PROCESS	BP	ATF4
GO_CELLULAR_RESPONSE_TO_AMINO_ACID_STARVATION	BP	ATF4
GO_REGULATION_OF_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_PRODUCTION	BP	ATF4
GO_PERK_MEDIATED_UNFOLDED_PROTEIN_RESPONSE	BP	ATF4
GO_MRNA_TRANSCRIPTION	BP	ATF4
GO_GLUCOSE_METABOLIC_PROCESS	BP	ATF4
GO_CELLULAR_RESPONSE_TO_STARVATION	BP	ATF4
GO_ORGANONITROGEN_COMPOUND_METABOLIC_PROCESS	BP	ATF4
GO_REGULATION_OF_CELLULAR_AMIDE_METABOLIC_PROCESS	BP	ATF4
GO_RESPONSE_TO_ARSENIC_CONTAINING_SUBSTANCE	BP	ATF4
GO_REGULATION_OF_OXIDATIVE_STRESS_INDUCED_CELL_DEATH	BP	ATF4
GO_REGULATION_OF_TRANSLATIONAL_INITIATION_IN_RESPONSE_TO_STRESS	BP	ATF4
GO_REGULATION_OF_DNA_TEMPLATED_TRANSCRIPTION_IN_RESPONSE_TO_STRESS	BP	ATF4
GO_REGULATION_OF_TRANSLATIONAL_INITIATION	BP	ATF4
GO_REGULATION_OF_OXIDATIVE_STRESS_INDUCED_NEURON_DEATH	BP	ATF4
GO_POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_I_PROMOTER	BP	ATF4
GO_CELLULAR_RESPONSE_TO_GLUCOSE_STARVATION	BP	ATF4
GO_REGULATION_OF_RESPONSE_TO_OXIDATIVE_STRESS	BP	ATF4
GO_HEXOSE_METABOLIC_PROCESS	BP	ATF4
GO_POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER_INVOLVED_IN_CELLULAR_RESPONSE_TO_CHEMICAL_STIMULUS	BP	ATF4
GO_NEGATIVE_REGULATION_OF_NEURON_DEATH	BP	ATF4
GO_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS	BP	ATF4
GO_POSITIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS	BP	ATF4
GO_RESPONSE_TO_MANGANESE_ION	BP	ATF4
GO_REGULATION_OF_POTASSIUM_ION_TRANSPORT	BP	ATF4
GO_POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER_IN_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS	BP	ATF4
GO_POSITIVE_REGULATION_OF_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_PRODUCTION	BP	ATF4
GO_MRNA_TRANSCRIPTION_FROM_RNA_POLYMERASE_II_PROMOTER	BP	ATF4
GO_INCLUSION_BODY	CC	ATF4
GO_DENDRITE_MEMBRANE	CC	ATF4
GO_NEURON_PROJECTION_MEMBRANE	CC	ATF4
GO_CORE_PROMOTER_BINDING	MF	ATF4
GO_LEUCINE_ZIPPER_DOMAIN_BINDING	MF	ATF4
GO_TRANSCRIPTIONAL_ACTIVATOR_ACTIVITY_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_BINDING	MF	ATF4
GO_LRR_DOMAIN_BINDING	MF	ATF4

Survival analysis of ATF4

Methods

Overall Survival

Disease Free Survival (RFS)

Group Cutoff

Median

Quartile

Custom

Cutoff-High(%)

Hazards Ratio (HR) Calculate the hazards ratio based on Cox PH Model.

95% Confidence Interval Add the 95% CI as dotted line.

Axis Units

Expression of ATF4

Pan cancer (TCGA) Cell line (ENCODE) In vitro differentiated cell (ENCODE) Primary cell (ENCODE) Tissue (NCBI) Normal tissue (GTEx) Cell line (CCLE)