Tutorial
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
E-Mail: yjhua2110@yahoo.com.cn
yangjh7@mail.sysu.edu.cn
The distinctive features of ChIPBase
1
Most comprehensive transcription factor binding maps
2
First platform for transcriptional regulation of lncRNAs
3
4
Most comprehensive TF->miRNA->Target networks
Expression profiles of lncRNAs/mRNAs in 22 tissues
5
Transcriptional regulation of other ncRNAs and mRNAs
6
Diverse tools/browsers for the transcriptional regulation
The core framework of ChIPBase
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
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
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
Browser
deepView-Provide Linkages of Searched Items
Browser
deepView-Information generated by ChIPBase
Browser
deepView-Information generated by ChIPBase
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
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
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
ChIP-Seq
browse-Results Interface
Get the
results in CSV
file
The total
number of
selected TF’s
binding sites
Choose the
number of
items
showing in
one page;
choose the
page you
want
Browse
Results
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
ChIP-Seq
Expression
pattern of TF
and target from
microarray data
Expression
pattern of TF
and target from
RNA-Seq data
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
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
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
ChIP-Seq
chipBrowse-Results Interface
Distribution
of selected
TF across the
genome
TF Binding
locations on
chromosomes
ChIP-Seq
chipBrowse-Results Interface
Distribution of
TF Binding Sites
associated with
transcription
start sites of
nearest genes
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
Choose a
reasonable
p-value
Star to browse
ChIP-Seq
chipGO Term-Results Interface
Link to
AmiGO for
further
information
about the
selected TF
and target
genes
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
Choose a
reasonable
p-value
Star to browse
ChIP-Seq
chipKEGG Term-Results Interface
Link to KEGG
for further
information
about the
selected TF
and target
genes
LncRNA
LncRNA-Startup Interface
Choose the researched
Clade, interested species
genome and database
Choose the specific TF
or ALL to check their
binding sites in lncRNAs
Input the Gene Symbol
of the interested lncRNA
LncRNA
LncRNA-Results Interface
Get the
results in CSV
file
The total number of
TF binding sites for
selected lncRNA
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
Click here to get
further information of
specific lncRNA and TF
in ChIPBase
LncRNA
LncRNA-Results Interface
lncRNA information
lncRNA Sequence
lncRNA expression pattern from 22 normal Tissues (RNA-Seq data)
MicroRNA
MicroRNA-Startup Interface
Choose the researched
Clade, interested species
genome and database
Choose the specific TF
or ALL to check their
binding sites in miRNAs
Select a type of miRNA
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
MicroRNA
MicroRNA-Results Interface
Click here to get
further information of
specific miRNA and TF
in ChIPBase
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
MicroRNA
TF-MiRNA-Target Network Interface
Select a type of miRNA
MicroRNA
TF-MiRNA-Target Network Interface
MicroRNA
TF-MiRNA-Target Network Interface
Select network
layout
Select miRNA
target
Zoom in/out or
move
networks
lncRNA Expression profile
lncRNA expression profile Interface
Input the lncRNA
you want to check
lncRNA expression profiles generated
from 22 tissues (RNA-Seq)
lncRNA Expression profile
lncRNA expression profile Interface
e.g. identify liver-specific lncRNAs by click liver tissue
Sort by table title
Sort by expression value by click the tissue
mRNA Expression profile
Protein-coding gene expression profile Interface
Protein-coding gene expression profiles generated
from 22 tissues (RNA-Seq)
mRNA Expression profile
Protein-coding gene expression profile Interface
Change expression
value
e.g. identify brain-specific lncRNAs by click brain tissue
Sort by table title
Sort by expression value by click the tissue
Protein
Protein-Startup Interface
Protein
Protein Interface
Click item
RNA-Seq
microarray
TFBScluster
TFBScluster-Startup Interface
Choose the researched
Choose
the researched
Clade,
interested
species
Clade,
interested
species
genome and database
genome and database
the TF TF
number in
ChooseSelect
the specific
a cluster
or ALL to check
their
binding sites in lncRNAs
Input the nearest
gene you want to
check
Input the Gene Symbol
of the interested lncRNA
TFBScluster
TFBScluster-Results Interface
Click here for
TFBS Cluster
information in
ChIPBase
Click the yellow
region to
rearrange the
results
AnnotatedTool
AnnotatedTool-Startup Interface
Enter ChIP-Seq data
Or Select ChIP-Seq data
AnnotatedTool
AnnotatedTool-Results Interface
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!!!