1. Regulation of Gene Expression
Ansuman Chattopadhyay, PhD
Head, Molecular Biology Information Services
Health Sciences Library System
University of Pittsburgh

2. Topics retrieve promoter sequences
determine transcription factor occupancy
browse through the epigenetic biochemical markers
Histone modifications, DNA methylation etc.,
-predict the location of enhancers, silencers and promoters
search for gene expression data from GEO using Correlation Engine

3. Tools identify promoter sequence(s) present in your gene of interest
Biobase Transpro
UCSC genome browser
predict transcription factor binding sites
Transfac (Biobase Match)
Browse through the epigenomic markers
ENCODE Human Epigenome Atlas IHEC

4. An excellent movie on transcription

5. Promoter, Enhancer and Silencer
Source:

6. More Movies @ HSLS MolBio Videos

7. Retrieve promoter sequence for a gene

9. InfoBooster: Molecular DBs

10. Myc,CD47 and CD274

11. Retrieve the promoter sequence of CD47 and PD-L1 genes
Identify Myc-binding sites present in the promoter sequences of CD47 and PD-L1
Retrieve the promoter sequence of CD47 and PD-L1 genes

13. Promoter Sequence Generic Promoter Seq Human Curated Promoter Seq
UCSC Genome Browser
Human Curated Promoter Seq
Biobase TransPro
mPROMDB
CSH TRED
Eukaryotic Promoter Database (EPD)

14. Link to the video tutorial:
Find sequence information for a gene
-genomic -promoter - intron-exon coordinates
-mRNA -protein
Resources
UCSC Genome Browser:
NCBI Entrez Gene:
Link to the video tutorial:

15. Fetching Promoters http://www.hsls.pitt.edu/molbio/videos/play?v=37

16. Promoter Sequence

17. Promoter Sequence

18. BIOBASE TransPro

19. BioBase Match

20. Biobase Match Search

21. Transcription Factors

22. Transcription Factor http://www.cisreg.ca/cgi-bin/tfe/home.pl

23. Transfac

24. Transcription Factor binding sites
Jonathan M. Keith (ed.), Bioinformatics, Volume II: Structure, Function and Applications, vol. 453, © 2008 Humana Press,

25. Information pertaining to a transcription factor

26. Transcription Factor - Myc

27. Create a Profile for Myc

28. Predicted Myc Binding Sites

29. Predicted Myc Binding Sites

30. Find Promoter Sequence
Retrieve promoter sequence for :
Human : BCL2, EGFR
C. elegans : let-23
Drosophila: son of sevenless
Yeast: fus3
Tips:
Go to UCSC genome browser
Search by gene name
Click on UCSC genes/Wormbase genes/Flybase genes
Click on Genomic sequence

33. Transcription Start Site (TSS)

34. Epigenome and Encyclopedia of DNA Elements Project

35. Spatiotemporal gene expression
EGFR
TP53

36. Illumina NextBio

37. A movie on regulated transcription

38. Epigenetic mechanisms
Source: NCBI

39. Genome in 3D

40. Chromatin Immuno-Precititation-Seq (ChIP-Seq)

41. Epigenetic Markers Landmark Paper:

42. Histone Modifications

43. Encode Project

44. ENCODE Project

45. Encode Cell Types http://genome.ucsc.edu/ENCODE/cellTypes.html

46. Predicted Myc Binding Sites

47. Promoter Database search.HSLS.MolBio

48. Promoter Database

49. Biobase Knowledge Library Promoter report

50. Link to the video tutorial:
Retrieve experimentally verified promoter sequence of a gene i.e. EGFR . What transcription factors binding sites are reported to be present in the gene regulatory region ?
Resources
Biobase Transpro:
Link to the video tutorial:

51. What transcription factors bind to a promoter sequence?

52. Find Transcription Factor Binding Sites
Basic Search:
TESS (Transcription Element Search System)
BIOBASE Match
Phylogenetic Footprinting:
ConSite
Footer

53. Transcription Factors (TF)
Database: Transfac-BioBase
Classification
Properties
Binding sites
Matrix

54. Transcription Factors occupancy analysis
Retrieve potential promoter sequence and predict transcription factors binding sites present in the promoter region:

55. Link to the video tutorial:
Retrieve potential promoter sequence of a yeast gene, fus3 and predict transcription factors binding sites present in the promoter region.
Resources
Biobase Match:
Link to the video tutorial:

56. Use Biobase Match program

57. Find conserved transcription factor binding sites
Footer
VISTA Tools
rVISTA
Whole Genome rVISTA

58. Footer Result Page

59. Browsing the ENCODE Data

60. Sec61g and EGFR
human chr7:54,801,956-55,305,954

61. EGFR and Sec61g

62. Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10.
EGFR and Sec61g
Role of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression.
Liao HJ, Carpenter G.
Mol Biol Cell Mar;18(3): Epub 2007 Jan 10.

63. UCSC Genome Browser: http://genome.ucsc.edu/
Convert the human genomic region between genes sec61g and EGFR into mouse, rat and zebra fish genomes
Resource
UCSC Genome Browser:
Link to the video tutorial:
File: UCSC_convert.swf

64. UCSC Genome Browser: Navigating a Genomic Region

65. UCSC Genome Browser: Navigating a Genomic Region

66. UCSC Genome Browser: Navigating a Genomic Region
What transcription factors bind in this region?

67. Sec61g and EGFR

68. UCSC Genome Browser: http://genome.ucsc.edu/
Identify promoter, enhancer and silencer sequences by browsing the epigenomic markers generated by the ENCODE project
Resource
UCSC Genome Browser:
Link to the video tutorial:

69. Cell Lines
K562
NHLF

70. Human Epigenome Atlas:

72. Regulome db Search rs rs

73. Regulome

75. Gene Expression Database Search By Correlation Engine (formerly NextBio)

77. NextBio Registration https://www.nextbio.com/b/register/register.nb

78. NextBio

79. NextBio

80. NextBio

81. NextBio Search

82. NextBio GeneList

83. Retrieve MicroRNA target genes

84. MicroRNA

85. MicroRNA Biology

86. Link to the video tutorial:
Identify miRNA(s) that have been reported or predicted to interact with
a gene.
Retrieve target genes of a miRNA
Resources
MiRNA database
Mirbase:
Target database
Mirtarbase:
Targetscan:
Miranda:
Pictar:
Link to the video tutorial:

87. Result comparison of miRNA prediction algorithms
ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets
PLOs One

88. Thank you! Any questions?
Carrie Iwema Ansuman Chattopadhyay