Identification of putative miR direct targets by microarray data

Glioma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by Sachet Shukla (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Identification of putative miR direct targets by microarray data. Broad Institute of MIT and Harvard. doi:10.7908/C18G8K3S

Overview

Introduction

This pipeline infers putative direct gene targets of miRs based on miR and gene expression profiles across multiple samples.

Summary

This pipeline use a relevance network approach to infer putative miR:mRNA regulatory connections. All miR:mRNA pairs that have correlations < -0.3 and have predicted interactions in three sequence prediction databases (Miranda, Pictar, Targetscan) define the final network.

Results

Significant miR:gene pairs

Figure 1. Get High-res Image All miR hubs with their strong anti-correlated genes and predicted interactions in three sequence prediction databases.

Table 1. Get Full Table List of miR:gene pairs with corr < -0.30 and predicted interactions in three sequence prediction databases.

miR	gene	Corr	prediction databases	miranda	pictar	targetscan	total
hsa-mir-22	CHD7	-0.497	miranda,pictar,targetscan	1	1	1	3
hsa-mir-34a	SOX4	-0.471	miranda,pictar,targetscan	1	1	1	3
hsa-mir-27a	FAM77C	-0.465	miranda,pictar,targetscan	1	1	1	3
hsa-mir-23a	PAK3	-0.441	miranda,pictar,targetscan	1	1	1	3
hsa-mir-9	FBN1	-0.430	miranda,pictar,targetscan	1	1	1	3
hsa-mir-152	CHD7	-0.429	miranda,pictar,targetscan	1	1	1	3
hsa-mir-34a	DPYSL4	-0.429	miranda,pictar,targetscan	1	1	1	3
hsa-mir-27a	CDK5R1	-0.424	miranda,pictar,targetscan	1	1	1	3
hsa-mir-9	P4HA2	-0.418	miranda,pictar,targetscan	1	1	1	3
hsa-mir-9	TGFBI	-0.414	miranda,pictar,targetscan	1	1	1	3

miR connections

Table 2. Get Full Table All miR hubs with their associated genes in the putative direct target network.

Mir	Number.of.Genes	Genes
hsa-mir-29a	21	ARVCF, BACH2, BCL11A, BLMH, DNMT3A, DNMT3B, EPHB3, HMGCS1, JARID1B, KCTD15, MYBL2, NASP, REV3L, RNF138, SOX12, SS18L1, TDG, TUBB, VASH2, ZBTB5,SETDB1
hsa-mir-9	17	ANXA2, CAPZA1, CAST, COL15A1, DSE, FBN1, GPR124, LDLRAP1, LEPRE1, P4HA2, RAI14, SHC1, SLC10A3, SLC25A24, TGFBI, TXNDC5,SDC2
hsa-mir-27a	13	AMOTL2, CA10, CABP1, CDK5R1, CHD7, EYA1, FAM77C, FRS3, PASK, PLCL2, RNF144A, SLCO5A1,RPS6KA5
hsa-mir-22	10	CHD7, CUL3, DGKI, H3F3A, JARID2, POGK, RSBN1, SNRK, SPEN,SEPHS1
hsa-mir-29b	10	BACH2, BLMH, DNMT3A, DNMT3B, JARID1B, MYBL2, TDG, TUBB, VASH2,NASP
hsa-mir-23a	9	B3GALT2, CDK5R1, CHD7, DNM3, MTSS1, PAK3, PKP4, SATB1,CAMTA1
hsa-mir-34a	7	E2F3, HN1, PDGFRA, SATB1, SOX4, TAF5,DPYSL4
hsa-mir-29c	5	BLMH, JARID1B, MYBL2, TUBB,BACH2
hsa-mir-155	4	CHD7, SATB1, ZNF238,CAMTA1
hsa-mir-222	4	POGZ, RIMS3, SHANK2,RP11-35N6.1

Gene connections

Table 3. Get Full Table All gene hubs with their associated miRs in the putative direct target network.

Gene	Number.of.Mirs	Mirs
CHD7	5	hsa-mir-155, hsa-mir-22, hsa-mir-23a, hsa-mir-27a,hsa-mir-152
BLMH	3	hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
TUBB	3	hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
CDK5R1	3	hsa-mir-23a, hsa-mir-27a,hsa-mir-152
MYBL2	3	hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
JARID1B	3	hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
SATB1	3	hsa-mir-23a, hsa-mir-34a,hsa-mir-155
BACH2	3	hsa-mir-29b, hsa-mir-29c,hsa-mir-29a
TDG	2	hsa-mir-29b,hsa-mir-29a
NASP	2	hsa-mir-29b,hsa-mir-29a

Methods & Data

Input

This section should list the files that were used as input.

Level 3 miR expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBMLGG-TP/22217161/GDAC_MergeDataFiles_12184404/GBMLGG-TP.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
Level 3 gene expression file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBMLGG-TP/22217225/GDAC_MergeDataFiles_12184409/GBMLGG-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt
miR:gene predicted interactions file = /xchip/cga/reference/miR_predictions/human_interactions.predicted.v2.txt
Miranda = microrna.org Aug 2010 release, Microcosm version 5
Pictar = version 1
Targetscan = release 5.2

Pearson corelation

Pairwise Pearson correlations coefficients between all miR:gene pairs are first computed. All genes that have correlation values less than the user-defined threshold (-0.3) with a particular miR and have been predicted as targets of that miR in three sequence based prediction databases: Miranda[1][2] Pictar[3][4], TargetScan [5][6][7] are identified as putative direct targets of that miR. We infer a direct target miR:gene network which comprises all such putative direct associations.

threshold = -0.3

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Betel D, Wilson M, Gabow A, Marks DS, Sander C, microRNA target predictions: The microRNA.org resource: targets and expression, Nucleic Acids Res 36:D149-53 (2008)

[2] John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS, miRanda: Human MicroRNA targets., PLoS Biol 3(7):e264 (2005)

[3] Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, Piedade ID, Gunsalus KC, Stoffel M, Rajewsky N, Combinatorial microRNA target predictions, Nature Genetics 37:495-500 (2005)

[4] Chen K, Rajewsky N, Natural selection on human microRNA binding sites inferred from SNP data., Nat Genet 38:1452-1456 (2006)

[5] Lewis BP, Burge CB, Bartel DP, Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets., Cell 120(120):15-20 (2005)

[6] Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP, MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing., Molecular Cell 27:91-105 (2007)

[7] Friedman RC, Farh KK, Burge CB, Bartel DP, Most Mammalian mRNAs Are Conserved Targets of MicroRNAs., Genome Research 19:92-105 (2009)

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