Back

DNA co-methylation networks outline the structure and remodeling dynamics of colorectal cancer epigenome

Mallona, I.; Ausso, S.; Diez-Villanueva, A.; Moreno, V.; Peinado, M. A.

2020-09-30 genomics
10.1101/428730 bioRxiv
Show abstract

Epigenomic plasticity is interconnected with chromatin structure and gene regulation. In tumor progression, orchestrated remodeling of genome organization accompanies the acquisition of malignant properties. DNA methylation, a key epigenetic mark extensively altered in cancer, is also linked to genome architecture and function. Based on this association, we postulate that the dissection of long-range co-methylation structure unveils cancer cells genome architecture remodeling. We applied network-modeling of DNA methylation co-variation in two colon cancer cohorts and found abundant and consistent transchromosomal structures in both normal and tumor tissue. Normal-tumor comparison indicated substantial remodeling of the epigenome covariation and revealed novel genomic compartments with a unique signature of DNA methylation rank inversion.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
eLife
● 5828 papers in training set
Top 8%
11.6%
Similar papers in this journal
2
Cell Reports
○ 1498 papers in training set
Top 3%
7.7%
Similar papers in this journal
3
Nature Communications
○ 5641 papers in training set
Top 23%
7.1%
Similar papers in this journal
4
Cell Genomics
○ 172 papers in training set
Top 0.5%
6.6%
Similar papers in this journal
5
Nucleic Acids Research
◐ 1281 papers in training set
Top 4%
5.4%
Similar papers in this journal
6
Molecular Cell
○ 350 papers in training set
Top 1%
4.7%
7
Genome Biology
○ 637 papers in training set
Top 3%
4.2%
8
Genome Research
● 468 papers in training set
Top 2%
3.9%
50% of probability mass above
9
Molecular Systems Biology
○ 162 papers in training set
Top 0.6%
3.4%
10
Cell
○ 431 papers in training set
Top 4%
2.7%
11
Genome Medicine
○ 183 papers in training set
Top 2%
2.3%
12
Cancer Cell
○ 42 papers in training set
Top 0.6%
2.3%
13
iScience
○ 1154 papers in training set
Top 14%
2.1%
14
Scientific Reports
○ 3612 papers in training set
Top 47%
2.1%
15
Nature Genetics
○ 286 papers in training set
Top 3%
2.1%
16
Frontiers in Genetics
○ 230 papers in training set
Top 2%
1.9%
17
Life Science Alliance
● 285 papers in training set
Top 4%
1.7%
18
Communications Biology
○ 993 papers in training set
Top 15%
1.7%
19
Bioinformatics
◐ 1204 papers in training set
Top 7%
1.7%
20
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 3%
1.7%
21
Genomics
○ 64 papers in training set
Top 0.9%
1.5%
22
Epigenetics & Chromatin
52 papers in training set
Top 0.4%
1.5%
23
Cell Reports Methods
○ 165 papers in training set
Top 2%
1.3%
24
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 3%
1.1%
25
Clinical Epigenetics
○ 60 papers in training set
Top 0.4%
1.1%
26
Epigenetics
○ 50 papers in training set
Top 0.5%
1.1%
27
PLOS Computational Biology
● 1863 papers in training set
Top 18%
1.0%
28
BMC Biology
○ 265 papers in training set
Top 5%
0.9%
29
PLOS Genetics
● 862 papers in training set
Top 12%
0.8%
30
Nature
○ 645 papers in training set
Top 11%
0.8%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.