cis-regulatory enrichment analysis in human, mouse and fly
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1 cis-regulatory enrichment analysis in human, mouse and fly Zeynep Kalender Atak, PhD Laboratory of Computational Biology VIB-KU Leuven Center for Brain & Disease Research
2 Laboratory of Computational Biology Deciphering gene control Genome control Undifferentiated tissue Differentiated cells
3
4 Gene signature co-expressed genes list of differentially expressed genes Enhancer signature TF ChIP-seq peaks ChIP-seq peaks against chromatin marks List of differentially acetylated / methylated regions Single-cell expression profile Cells Genes expression profile of genes across single cells SCENIC
5 iregulon cis-regulatory sequence analysis on gene signatures
6 iregulon cis-regulatory sequence analysis on gene signatures Set of co-expressed genes What are the key transcription factors (TFs) and the direct target genes (TGs)? What are the co-factors and their direct target genes? Janky & Verfaillie et al. (2014), PLoS Computational Biology
7 iregulon cis-regulatory sequence analysis on gene signatures TG4 TG2 TF2 TG3 TG1 Set of co-expressed genes TF1 Janky & Verfaillie et al. (2014), PLoS Computational Biology
8 iregulon cis-regulatory sequence analysis on gene signatures candidate motifs motif clustering (CRMs) cross-species conservation whole-genome rankings gene set enrichment AUC PWMs 1797 human TFs RANKING RECOVERY TG4 TG2 TF2 TG3 TG1 TF1 M4 MOTIF2TF MAPPING TF6 TF7 TF5 M3 M1 TF4 M2 TF5 TF3 1) motif-tf annotations 2) in input 3) orthology 4) motif similarity Janky & Verfaillie et al. (2014), PLoS Computational Biology TF1 TF2
9 Set of differentially expressed genes Master Regulons & cofactors Human & mouse & fly ChIP-derived targets TF regulon Set of mirna target genes mirna and TF co-regulons Functional network cluster Regulatory network cluster One TF node TF meta-targetome Janky & Verfaillie et al. (2014), PLoS Computational Biology
10 Using iregulon to decipher the p53 targetome Set of differentially expressed genes Master Regulons & cofactors
11 iregulon Using iregulon to decipher the p53 targetome the guardian of genome one of the most studied TFs downstream GRN is not clear Bieging & Attardi et al. (2012), Trends in Cell Biology
12 iregulon Using iregulon to decipher the p53 targetome Nutlin-3a 801 up-regulated genes MCF7 cells 790 downregulated genes Janky & Verfaillie et al. (2014), PLoS Computational Biology
13 iregulon Using iregulon to decipher the p53 targetome 801 up-regulated genes iregulon results panel
14 iregulon Using iregulon to decipher the p53 targetome Motifs
15 iregulon Using iregulon to decipher the p53 targetome Tracks
16 iregulon Using iregulon to decipher the p53 targetome
17 iregulon Using iregulon to decipher the p53 targetome
18 iregulon Using iregulon to decipher the p53 targetome Nutlin-3a 801 up-regulated genes TF NES # of targets # of motifs TP AP1 (FOS/JUN) FOX NFY TF NES # of targets # of motifs MCF7 cells 790 downregulated genes E2F NFY KDM2B TP53 master regulator; AP1, FOX and NFY as co-factors No TP53 motif in the repressive network Janky & Verfaillie et al. (2014), PLoS Computational Biology
19 iregulon Using iregulon to decipher the p53 targetome
20 iregulon Validation with p53 ChIP-seq with Nutlin-3a ChIP-seq p53 Stimulated ChIP-seq p53 Input RNA-seq p53 Stimulated RNA-seq p53 Not stimulated Refseq Genes CDKN1A
21 iregulon Using iregulon to decipher the p53 targetome 100 p53 direct targets are enriched in ChIPseq peaks 80 are novel targets Janky & Verfaillie et al. (2014), PLoS Computational Biology
22 iregulon More case studies in
23 i-cistarget cis-regulatory sequence analysis on enhancer signatures
24 i-cistarget cis-regulatory sequence analysis on enhancer signatures Imrichová et al. (2015), Nucleic Acids Research
25 i-cistarget cis-regulatory sequence analysis on enhancer signatures Similar rank & recovery approach to iregulon Relies on candidate regulatory regions rather than genes Imrichová et al. (2015), Nucleic Acids Research
26 TF ChIP-seq peaks The motifs and TF ChIP-seq tracks of the ChIP'ped factor Motifs and ChIP-seq tracks of co-factors Correlated DHS/Faire/ Histone marks Set of differentially active regions The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks A set of genes The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks
27 Analyzing GATA1 ChIP-seq data on K562 cell line TF ChIP-seq peaks The motifs and TF ChIP-seq tracks of the ChIP'ped factor Motifs and ChIP-seq tracks of co-factors Correlated DHS/Faire/ Histone marks
28 i-cistarget Analyzing GATA1 ChIP-seq data on K562 cell line hg19, mm9, dm3 bed file gene symbol (HGNC) i-cistarget region IDs Imrichová et al. (2015), Nucleic Acids Research
29 i-cistarget Analyzing GATA1 ChIP-seq data on K562 cell line GATA motifs DHS regions on K562 cell line
30 TF ChIP-seq peaks The motifs and TF ChIP-seq tracks of the ChIP'ped factor Motifs and ChIP-seq tracks of co-factors Correlated DHS/Faire/ Histone marks Set of differentially active regions The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks A set of genes The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks
31 Melanoma phenotype switching Set of differentially active regions The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks
32 i-cistarget Identifying master regulators of melanoma phenotype switching Malignant melanoma development is characterized by a bistable switch between different states Invasive and proliferative states were described in melanoma cell cultures (Hoek et al., 2008) We observed them also in tumour biopsies (TCGA: RNA-seq for 375 samples) Verfaillie & Imrichová & Kalender Atak et al. (2015), Nature Communications
33 i-cistarget Identifying master regulators of melanoma phenotype switching ChIP-seq against H3K27Ac in 9 proliferative short-term cultures ChIP-seq against H3K27Ac in 2 invasive short-term cultures differentially active regions 6669 proliferative regions invasive regions Verfaillie & Imrichová & Kalender Atak et al. (2015), Nature Communications
34 TF ChIP-seq peaks The motifs and TF ChIP-seq tracks of the ChIP'ped factor Motifs and ChIP-seq tracks of co-factors Correlated DHS/Faire/ Histone marks Set of differentially active regions The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks A set of genes The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks
35 p53 targetome revisited A set of genes The most correlated motifs and TF ChIP-seq tracks Correlated DHS/Faire/ Histone marks
36 i-cistarget p53 targetome revisited Treatment of MCF-7 cells with Nutlin-3a Library Preparation & Sequencing Differential Expression Analysis & Filtering 801 up (790 down) Control (2x) / Nutlin-3a (2x) million reads/sample FDR<0.05 & log2fc >1 Rank Feature NES Logo 1 transfac_pro-m01656 Description: V$P63_01 Possible TFs: TP63, TP53, TP candidate regions 2 taipale-racatgycnngrcatgty-tp53-dbd Description: RACATGYCNNGRCATGTY-Tp53-DBD Possible TFs: TP63, TP transfac_pro-m01651 Description: V$P53_03 Possible TFs: TP63, TP53, TP lcbtfbs_mcf7_p53_nutlin Description: lcbtfbs_mcf7_p53_nutlin ENCFF001WPZ Description: DNase-seq on human MCF
37 i-cistarget p53 targetome revisited ChIP-seq p53 Stimulated ChIP-seq p53 Input RNA-seq p53 Stimulated RNA-seq p53 Not stimulated Refseq Genes CDKN1A
38 i-cistarget More case studies in apps/lcb/i-cistarget-nar/index.php#examples
39 SCENIC Single Cell regulatory Network Inference and Clustering
40 SCENIC Single Cell regulatory Network Inference and Clustering Aibar et al., Submitted
41 SCENIC Mapping regulatory cell states of melanoma with SCENIC tsne on expression data tsne on binary regulon activity SCENIC 1252 malignant cells from 14 biopsies (Tirosh, I. et al. (2016) Science)
42 SCENIC Mapping regulatory cell states of melanoma with SCENIC tsne on expression data tsne on binary regulon activity SCENIC 1252 malignant cells from 14 biopsies (Tirosh, I. et al. (2016) Science) Containing cancer cells from 10 different tumors
43 SCENIC Mapping regulatory cell states of melanoma with SCENIC
44 SCENIC Mapping regulatory cell states of melanoma with SCENIC
45 SCENIC Mapping regulatory cell states of melanoma with SCENIC
46 LCB aertslab.org
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