1. General

The general information (for example, class, superfamily, family, description, length, the link to Dfam database and consensus sequence) of ERV elements comes from the following references:  
[1]UCSC Table Browser. group Repeats track RrepeatMasker.[2022-11-24]. http://www.genome.ucsc.edu/cgi-bin/hgTables  
[2]Dfam.[2022-1-2]. https://dfam.org/home  
[3]Wheeler TJ, et al. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 2013 Jan;41(Database issue):D70-82  
[4]Repbase.[2022-1-2]. https://www.girinst.org/repbase/  
[5]Jurka J, et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res, 2005;110(1-4):462-7

2. Expression profile

Stage	Replicates	Project ID in NCBI GEO database
oocytes	6	GSE36552,GSE44183
pronuclei	3	GSE44183
zygote	5	GSE36552,GSE44183
2-cell	9	GSE36552,GSE44183
4-cell	16	GSE36552,GSE44183
8-cell	31	GSE36552,GSE44183
morula	19	GSE36552,GSE44183
blastocyst	30	GSE36552
hESC.passage#0	6	GSE36552
hESC.passage#10	26	GSE36552

References: Goke, J., et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell, 2015. 16(2): p.135-41

Tissue	Female	Male
Adipose_Subcutaneous	121	312
Adipose_Visceral_Omentum	81	223
Adrenal_Gland	64	145
Artery_Aorta	85	221
Artery_Coronary	55	132
Artery_Tibial	105	294
Brain_Amygdala	19	65
Brain_Anterior_cingulate_cortex_BA24	20	78
Brain_Caudate_basal_ganglia	31	108
Brain_Cerebellar_Hemisphere	29	97
Brain_Cerebellum	37	116
Brain_Cortex	33	107
Brain_Frontal_Cortex_BA9	28	99
Brain_Hippocampus	27	87
Brain_Hypothalamus	24	90
Brain_Nucleus_accumbens_basal_ganglia	29	102
Brain_Putamen_basal_ganglia	24	86
Brain_Spinal_cord_cervical_c1	27	68
Brain_Substantia_nigra	22	59
Breast_Mammary_Tissue	85	202
Cells_EBVtransformed_lymphocytes	42	117
Cells_Transformed_fibroblasts	103	282
Colon_Sigmoid	61	149
Colon_Transverse	80	194
Esophagus_Gastroesophageal_Junction	59	152
Esophagus_Mucosa	106	283
Esophagus_Muscularis	89	245
Heart_Atrial_Appendage	66	190
Heart_Left_Ventricle	65	190
Kidney_Cortex	6	31
Liver	39	114
Lung	98	291
Minor_Salivary_Gland	19	57
Muscle_Skeletal	143	389
Nerve_Tibial	95	274
Ovary	97	NA
Pancreas	67	166
Pituitary	29	103
Prostate	NA	104
Skin_Not_Sun_Exposed_Suprapubic	85	245
Skin_Sun_Exposed_Lower_leg	115	314
Small_Intestine_Terminal_Ileum	37	88
Spleen	44	104
Stomach	81	192
Testis	NA	172
Thyroid	99	286
Uterus	82	NA
Vagina	95	NA
Whole_Blood	130	354

References: Gireesh K. Bogu, et al. Atlas of transcriptionally active transposable elements in human adult tissues.[2022-12-6]. 

https://www.biorxiv.org/content/10.1101/714212v1.full

Cancer cell	N
lung	165
haematopoietic_and_lymphoid_tissue	163
central_nervous_system	61
large_intestine	55
breast	50
skin	49
ovary	44
pancreas	41
fibroblast	35
stomach	33
upper_aerodigestive_tract	30
kidney	29
endometrium	27
oesophagus	25
liver	23
urinary_tract	19
bone	18
soft_tissue	17
autonomic_ganglia	16
thyroid	9
biliary_tract	7
pleura	7
prostate	6
salivary_gland	2
small_intestine	1

References: Ghandi, M., et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature, 2019. 569(7757): p. 503-508

3. Differential expression

N	Study	Cancer	Solid normal tissues	Primary tumor tissues
1	BRCA	Breast_invasive_carcinoma	113	1089
2	COREAD	corectal_cancer	51	631
3	LUAD	Lung_adenocarcinoma	59	522
4	UCEC	Uterine_Corpus_Endometrial_Carcinoma	35	547
5	KIRC	Kidney_renal_clear_cell_carcinoma	72	534
6	HNSC	Head_and_Neck_squamous_cell_carcinoma	44	499
7	THCA	Thyroid_carcinoma	58	501
8	LUSC	Lung_squamous_cell_carcinoma	49	502
9	PRAD	Prostate_adenocarcinoma	52	496
10	STAD	Stomach_adenocarcinoma	32	375
11	BLCA	Bladder_Urothelial_Carcinoma	19	411
12	LIHC	Liver_hepatocellular_carcinoma	50	371

References: National Institutes of Health The Cancer Genome Atlas (TCGA). dbGaP Study Accession: phs000178.v11.p8.[2022-11-24].https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178.v11.p8  
The stage and histological type information of TCGA patients comes from the following reference: Liu J, et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr 5;173(2):400-416.e11

4. Survival analysis

The survival information including OS and OS time of TCGA patients comes from the following reference: Liu J, et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr 5;173(2):400-416.e11

5. Correlation

The correlation result is based on TCGA primary cancer tissues RNA-seq dataset.