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OmicsX: a web server for integrated OMICS analysis

Pan, J.; Qian, J.; Zhang, H.

2019-09-09 bioinformatics
10.1101/755918 bioRxiv
Show abstract

High-throughput omic data sets like genomics, transcriptomics, proteomics, glycomics, lipitomics, metabolomics, and modified forms of the biological molecules have been generated to investigate biological mechanisms. Accordingly, bioinformatic methods and tools have been developed and applied to analyze the omics data for different purposes. However, a lack of comparison and integration tools impedes the deep exploration of multi-omics data. OmicsX is a user-friendly web server for integration and comparison of different omic datasets with optional sample annotation information. The tool includes modules for gene-wise correlation, sample-wise correlation, subtype clustering, and differential expression. OmicsX provides researchers the analysis results with visualization, searching, and data downloading, and help to suggest the biological indications from the comparison of different omic data.\n\nAvailability and implementationhttp://bioinfo.wilmer.jhu.edu/OmicsX/

Matching journals

The top 11 journals account for 50% of the predicted probability mass.

1
PLOS ONE
● 5266 papers in training set
Top 20%
8.0%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 3%
6.8%
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3
BMC Bioinformatics
○ 457 papers in training set
Top 1%
6.4%
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4
Briefings in Bioinformatics
◐ 354 papers in training set
Top 1%
6.4%
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5
PLOS Computational Biology
● 1863 papers in training set
Top 8%
4.4%
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6
Scientific Reports
○ 3612 papers in training set
Top 24%
4.1%
7
Frontiers in Genetics
○ 230 papers in training set
Top 0.9%
3.6%
8
PeerJ
◐ 308 papers in training set
Top 2%
3.6%
9
Database
◐ 61 papers in training set
Top 0.2%
3.2%
10
Genes
○ 144 papers in training set
Top 1%
2.5%
11
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 2%
2.4%
50% of probability mass above
12
BMC Genomics
○ 406 papers in training set
Top 4%
1.8%
13
Genomics
○ 64 papers in training set
Top 0.7%
1.8%
14
Gigabyte
● 62 papers in training set
Top 0.6%
1.8%
15
PROTEOMICS
○ 43 papers in training set
Top 0.4%
1.7%
16
International Journal of Molecular Sciences
○ 494 papers in training set
Top 8%
1.7%
17
Computers in Biology and Medicine
○ 128 papers in training set
Top 3%
1.5%
18
F1000Research
○ 88 papers in training set
Top 2%
1.4%
19
Biology
○ 45 papers in training set
Top 0.3%
1.1%
20
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
1.1%
21
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
22
Animals
○ 23 papers in training set
Top 0.6%
1.1%
23
Computational Biology and Chemistry
○ 28 papers in training set
Top 0.6%
1.1%
24
Gene Reports
○ 14 papers in training set
Top 0.5%
1.1%
25
BMC Medical Genomics
○ 50 papers in training set
Top 0.9%
1.1%
26
International Journal of Environmental Research and Public Health
○ 128 papers in training set
Top 4%
1.0%
27
Frontiers in Bioinformatics
○ 49 papers in training set
Top 1%
1.0%
28
Cancers
○ 213 papers in training set
Top 5%
0.9%
29
BioData Mining
○ 22 papers in training set
Top 0.6%
0.9%
30
Biosystems
○ 31 papers in training set
Top 0.5%
0.9%

"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.