(Q33776339)

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TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information

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scholarly article

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Europe PubMed Central

PubMed publication ID

29 July 2017

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information (English)

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Gene Set Enrichment

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based on heuristic

inferred from title

author name string

Qi Liu

1

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Yejun Tan

2

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Europe PubMed Central

PubMed publication ID

29 July 2017

Tao Huang

3

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Guohui Ding

4

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Zhidong Tu

5

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Lei Liu

6

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Yixue Li

7

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Hongyue Dai

8

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

Lu Xie

9

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

publication date

14 December 2010

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Europe PubMed Central

PubMed publication ID

29 July 2017

BMC Bioinformatics

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Europe PubMed Central

PubMed publication ID

29 July 2017

11 Suppl 11

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Europe PubMed Central

PubMed publication ID

29 July 2017

S5

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Europe PubMed Central

PubMed publication ID

29 July 2017

copyright license

Creative Commons Attribution 2.0 Generic

1 December 2010

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April 2022 Public Data File from Crossref

copyright status

0 references

https://scigraph.springernature.com/pub.10.1186/1471-2105-11-s11-s5

0 references

FuncBase: a resource for quantitative gene function annotation

1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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30 October 2018

Identifiers

10.1186/1471-2105-11-S11-S5

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

DBLP publication ID

journals/bmcbi/LiuTHDTLLDX10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 July 2017

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