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Open Access Highly Accessed Research article

Preferential regulation of miRNA targets by environmental chemicals in the human genome

Xudong Wu123* and Yijiang Song2

Author Affiliations

1 Key laboratory of Photosynthesis and Environmental Molecular Physiology, the Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

2 Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, 325035, China

3 State key laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China

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BMC Genomics 2011, 12:244  doi:10.1186/1471-2164-12-244

Published: 18 May 2011

Additional files

Additional file 1:

Table S1: The 42,770 regulatory relationships among 1938 chemicals and 9,692 human protein-coding genes.

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Additional file 2:

Table S2: The list of miRNA targets predicted by PicTar, TargetScan5.1, both programs of PicTar and TargetScan5.1 (intersections), and by PITA.

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Additional file 3:

Figure S1: miRNA targets are enriched among EC-genes in Mus musculus and Rattus norvegicus. This figure shows the proportion of miRNA targets predicted (A) by Mus musculus TargetScan5.1, (B) by Mus musculus PITA and (C) by Rattus norvegicus TargetScan5.1. As there are no miRNA targets from the PicTar prediction for both species and PITA prediction for Rattus norvegicus, this figure shows the proportion of miRNA targets predicted by TargetScan5.1 and the Rattus norvegicus PITA. The horizontal lines above histogram bars represent the proportion of miRNA targets using genes with human orthologs as background.

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Additional file 4:

Table S3: The 4,126 papers investigating the expression profiles of human genes in response to ECs.

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Additional file 5:

Figure S2: miRNA targets are enriched among human EC-genes after filtering out the cancer-related genes in simulations. This figure shows the proportion of miRNA targets predicted by PicTar, TargetScan5.1, both programs of PicTar and TargetScan5.1 (intersections), and PITA. The horizontal lines above the histogram bars represent the proportion of miRNA targets using genes with mouse orthologs as background.

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Additional file 6:

Figure S3: miRNA targets are enriched among human EC-genes after controlling for potential false-negatives of non-EC-genes. This figure shows the proportion of miRNA targets predicted by PicTar, TargetScan5.1, both programs of PicTar and TargetScan5.1 (intersections), and PITA. The horizontal lines above the histogram bars represent the proportion of miRNA targets using genes with mouse orthologs as background.

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Additional file 7:

Figure S4: miRNA targets are enriched among human EC-genes in 11 raw-data-based microarray datasets. This figure shows the proportion of miRNA targets between differentially vs. non-differentially regulated genes where (A) A549 cells treated with asbestos, (B) Beas-2B cells treated with asbestos, (C) Dendritic cells treated with AM580, (D) Dendritic cells treated with rosiglitazone, (E) Epithelia cells treated with selenium, (F) Epithelia cells treated with Vitamin E, (G) Stromal cells treated with selenium, (H) HCT116 cells treated with fluorouracil, (I) HCT116 cells treated with SN38, (J) HepG2 cells treated with NMN and (K) HepG2 cells treated with phenol. The horizontal lines above the histogram bars represent the proportion of miRNA targets using genes with mouse orthologs as background.

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Additional file 8:

Table S4: The 1,842 pairs of significantly concurrent EC-miRNA based on the TargetScan5.1.

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Additional file 9:

Table S5: The 14 topological modules with their miRNAs and ECs. The number in the bracket indicates the number of miRNAs associated with the corresponding disease categories.

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Additional file 10:

Figure S5: miRNA targets are enriched among human EC-associated genes by STITCH2.0. This figure shows the proportion of miRNA targets predicted (A) by PicTar, (B) by TargetScan5.1, (C) by both programs of PicTar and TargetScan5.1 (intersections), and (D) by PITA. The horizontal lines above the histogram bars represent the proportion of miRNA targets using genes with mouse orthologs as background.

Format: JPEG Size: 423KB Download file

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