1. Tutorial E-Mail: yjhua2110@yahoo.com.cnyjhua2110@yahoo.com.cn yangjh7@mail.sysu.edu.cn ChIPBase: decoding the transcriptional regulation of lncRNAs, mRNAs and miRNAs from ChIP-Seq data © 2012, Jian-Hua Yang, The Qu lab at Sun Yat-sen University

2. The distinctive features of ChIPBase Most comprehensive transcription factor binding maps 1 2 First platform for transcriptional regulation of lncRNAs 3 Most comprehensive TF->miRNA->Target networks 4 Expression profiles of lncRNAs/mRNAs in 22 tissues 5 Transcriptional regulation of other ncRNAs and mRNAs 6 Diverse tools/browsers for the transcriptional regulation

3. The core framework of ChIPBase

4. Browser deepView-Startup Interface Choose the researched Clade Choose the interested species genome Choose the database Input the interested genomic region, gene name, lncRNA name and miRNA name. Start to search the results Use the official example to test the use of deepView

5. Browser deepView-Browser Interface Magnify and Minify the demonstrative Box Move the sequence bar and adjust the box width Reveal the genomic position of input information on startup interface; Redirect the position and rebrowse Demonstrative Box: display information according to the input and track options

6. Browser deepView-Browser Interface fff Choose interested track items to display in demonstrative box Link to UCSC Genome Browser to check the similar results Selected track items

7. Browser deepView-Provide Linkages of Searched Items

8. Browser deepView-Information generated by ChIPBase

9. Browser deepView-Information generated by ChIPBase

10. Browser genomeView-Startup Interface Choose the researched Clade, interested species genome and database Choose the transcription factor to be browsed across the genome selected above Adjust the height of image displaying browse results

11. Browser genomeView-Browser Interface Click here to generate PDF of results image below Image of browse results: the selected TF’s binding sites are located on the chromosomes (blue) across the genome Click the binding sites region to get further information from deepView

12. ChIP-Seq browse-Startup Interface Choose the researched Clade, interested species genome and database Choose the transcription factor that you want to know it binding sites across the genome selected above Star to browse

13. ChIP-Seq browse-Results Interface The total number of selected TF’s binding sites Get the results in CSV file Choose the number of items showing in one page; choose the page you want Browse Results

14. ChIP-Seq browse-Results Interface Click on the yellow region to rearrange the results Click here to get further information: ChIP-Seq region information, Nearest gene information, Nearest gene expression pattern and References

15. ChIP-Seq Expression pattern of TF and target from microarray data Expression pattern of TF and target from RNA-Seq data

16. ChIP-Seq chipBrowse-Startup Interface Choose the researched Clade, interested species genome and database Choose the transcription factor that you want to know it features Star to browse

17. ChIP-Seq chipBrowse-Results Interface The results include three features of selected TF and its binding sites Functional information of TF in ChIPBase Functional information of TF in AmiGO

18. ChIP-Seq chipBrowse-Results Interface The results include three features of selected TF and its binding sites Expression profiles of TF from RNA-Seq data from 22 normal tissues

19. ChIP-Seq chipBrowse-Results Interface Distribution of selected TF across the genome TF Binding locations on chromosomes

20. ChIP-Seq chipBrowse-Results Interface Distribution of TF Binding Sites associated with transcription start sites of nearest genes

21. ChIP-Seq chipGO Term-Startup Interface Choose the researched Clade, interested species genome and database Choose the transcription factor that you want to involve into GO Analysis Star to browse Choose a reasonable p-value

22. ChIP-Seq chipGO Term-Results Interface Link to AmiGO for further information about the selected TF and target genes

23. ChIP-Seq chipKEGG Term-Startup Interface Choose the researched Clade, interested species genome and database Choose the transcription factor that you want to involve into KEGG Analysis Star to browse Choose a reasonable p-value

24. ChIP-Seq chipKEGG Term-Results Interface Link to KEGG for further information about the selected TF and target genes

25. LncRNA LncRNA-Startup Interface Choose the researched Clade, interested species genome and database Input the Gene Symbol of the interested lncRNA Choose the specific TF or ALL to check their binding sites in lncRNAs

26. LncRNA LncRNA-Results Interface The total number of TF binding sites for selected lncRNA Get the results in CSV file Click here to get further information of specific lncRNA and TF in ChIPBase There is only one recognition domain for this TF (EWS-ERG)in lncRNA(lncRNA2314-1); Click the number to check the details about this domain

27. LncRNA LncRNA-Results Interface lncRNA information lncRNA Sequence lncRNA expression pattern from 22 normal Tissues (RNA-Seq data)

28. MicroRNA MicroRNA-Startup Interface Choose the researched Clade, interested species genome and database Select a type of miRNA Choose the specific TF or ALL to check their binding sites in miRNAs

29. MicroRNA MicroRNA-Results Interface Click here to get further information of specific miRNA and TF in ChIPBase There is only one recognition domain for this TF (AR) within this miRNA; Click the number to check the details about this domain

30. MicroRNA MicroRNA-Results Interface Click here to get further information of specific miRNA and TF in ChIPBase

31. MicroRNA MicroRNA-Results Interface There is only one recognition domain for this TF (AR) within this miRNA; Click the number to check the details about this domain Expression pattern of TF in 22 normal tissues

32. MicroRNA TF-MiRNA-Target Network Interface Select a type of miRNA

33. MicroRNA TF-MiRNA-Target Network Interface

34. MicroRNA TF-MiRNA-Target Network Interface Select miRNA target Select network layout Zoom in/out or move networks

35. lncRNA Expression profile lncRNA expression profile Interface Input the lncRNA you want to check lncRNA expression profiles generated from 22 tissues (RNA-Seq)

36. lncRNA Expression profile lncRNA expression profile Interface Sort by table titleSort by expression value by click the tissue e.g. identify liver-specific lncRNAs by click liver tissue

37. mRNA Expression profile Protein-coding gene expression profile Interface Protein-coding gene expression profiles generated from 22 tissues (RNA-Seq)

38. mRNA Expression profile Protein-coding gene expression profile Interface Sort by table titleSort by expression value by click the tissue Change expression value e.g. identify brain-specific lncRNAs by click brain tissue

39. Protein Protein-Startup Interface

40. Protein Protein Interface Click item RNA-Seqmicroarray

41. TFBScluster TFBScluster-Startup Interface Choose the researched Clade, interested species genome and database Input the Gene Symbol of the interested lncRNA Choose the specific TF or ALL to check their binding sites in lncRNAs Choose the researched Clade, interested species genome and database Select the TF number in a cluster Input the nearest gene you want to check

42. TFBScluster TFBScluster-Results Interface Click here for TFBS Cluster information in ChIPBase Click the yellow region to rearrange the results

43. AnnotatedTool AnnotatedTool-Startup Interface Enter ChIP-Seq data Or Select ChIP-Seq data

44. AnnotatedTool AnnotatedTool-Results Interface

45. Congratulations! you have already finished the tutorial of ChIPBase! Now it’s time for you to try it in your own research projects. Good luck! Thanks for your interest in our ChIPBase!!!