Additional file 1 of Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

Supplementary tables and figures. Additional Table S1–S3. TableS1: Downloaded data from ENCODE (GM12878/K562). TableS2 : Details of downloaded data control (GM12878/K562). TableS3: Top five significant GO categories for the active cluster in both cell lines. Additional Figures S1–S25. FigS1: TSSs assigned to clusters according to biclustering algorithm. FigS2: Biclustering result of active TSS in K562 cell-line. FigS3: Biclustering result of inactive TSS in K562 cell-line. FigS4: TSSs assigned to clusters according to biclustering algorithm based on CAGE tags. FigS5: Proportion of each cluster among all assigned promoters. FigS6: Expression measures and possible covariates associated to individual clusters in K562 cell line. FigS7: NFY co-binding pattern in GM12878 cell line. FigS8: NFY co-binding pattern in K562 cell line. FigS9: TF motif hits in promoters in GM12878 cell line. FigS10: TF motif hits in promoters in K562 cell line. FigS11: Biclustering results based on CAGE tags. FigS12: Validation of NFY, USF, and CTCF clusters in HeLa cells. FigS13: Validation of NFY, USF, and CTCF clusters in GM12878 cells based on CAGE tags. FigS14: Validation of NFY, USF, and CTCF clusters in K562 cells based on CAGE tags. FigS15: Examples of inactive TSS embedded in an active gene. FigS16: Example of promoter bound either by NFY or USF in the two cell lines. FigS17: Transcript type and function analysis for genes in each cluster. FigS18: Histone modifications and transcription factors significantly contributing to gene expression. FigS19: Binding combinatorics in E-box containing promoters in K562 cell line. FigS20: Binding patterns of NFYA, FOS and SP1 compared to motif occurrence in K562 cell line. FigS21: Sum of square errors and coefficient in k-means clustering under different number of clusters, for active/inactive TSSs for GM12878/K562 cell line. FigS22: Biclustering methods. FigS23: Comparison of biclustering and k-means methods. FigS24: Example of a promoter whit multiple CAGE tag annotations. FigS25: Overview of promoters definition based on CAGE tags. (PDF 11,502 kb)