Gonzalo Gómez, PhD. [email protected]
Madrid, June 31st, 2007.
::: The Connectivity Map - cMap -
Course on Functional Analysis
Bioinformatics Unit CNIO
The Connectivity Map - cMap -
::: Introduction.
MIT Broad Institute
164 small molecules loaded
10nm, 100nm, 1 µM, 10 µM 6 & 12 hours treatment
Breast, prostate, leukemia and melanoma cell lines
cMap
Lamb et al. Science 29 September 2006:
Vol. 313. no. 5795, pp. 1929 - 1935
The Connectivity Map - cMap -
::: Introduction.
cMap applications :::
A hypotheses generating tool
The Connectivity Map - cMap -
::: Introduction.
Example :::
Molecular signature strongly induced by
drug A
Molecular signature weakly induced by
drug B
Drug C has no effects on molecular signature
Molecular signature strongly repressed by
drug D.
Perturbagen: Any modality, such as addition of a small molecule or introduction of a genetic reagent (eg shRNA). Perturbagens (or groups of closely related perturbagens) are identified in cmap by their cmap name. A single perturbagen may be represented by multiple instances.
Instances: A treatment and control pair and the list of probe sets ordered by their extent of differential expression between this treatment and control pair. The instance is the basic unit of data and metadata in cmap. Each instance is uniquely identified by an instance_id. Every instance has a number of attributes including a unique identifier ( ie instance_id), the batch in which it was produced, the cmap name of the treatment, the source of that treatment, the concentration of that treatment, the cmap cell line used, and the scan numbers for the treatment and its control(s).
The Connectivity Map - cMap -
::: Introduction.
cMap Nomenclature :::
The Connectivity Map - cMap -
::: Introduction.
K-S test :::
The Kolmogorov–Smirnov test is used to determine whether two underlying one-dimensional probability distributions differ, or whether an underlying probability distribution differs from a hypothesized distribution, in either case based on finite samples.
The one-sample KS test compares the empirical distribution function with the cumulative distribution functionspecified by the null hypothesis. The main applications are testing goodness of fit with the normal and uniform distributions.
The two-sample KS test is one of the most useful and general nonparametric methods for comparing two samples, as it is sensitive to differences in both location and shape of the empirical cumulative distribution functions of the two samples.
Instance 1 distribution
Num
ber of genes Gene Expression Level
Up tag list distribution
Down tag list distribution
Instance 2 distribution
Num
ber of genes
Gene Expression Level
Up tag list distribution
Down tag list distribution
etc.
The Connectivity Map - cMap -
::: cMap Web Tool.
Accession :::
http://www.broad.mit.edu/cmap/
Registration
The Connectivity Map - cMap - Main Window :::
::: cMap Web Tool.
The Connectivity Map - cMap - Help Tab :::
::: cMap Web Tool.
Quick and tmp
The Connectivity Map - cMap - Query tab :::
::: cMap Web Tool.
Load, store signatures and save results
Preloaded data
Build a internal signature from a number (until 3) of different instances on the fly
The Connectivity Map - cMap - Quick Query :::
For human signatures: NetAffx
For non human signatures: 1) Homologene (to Unigene) 2) NetAffx
.grp files HG-U133A identifiers
::: Query Tab.
The Connectivity Map - cMap -
::: .grp Format
Remember Affy HG-U133A identifiers !!!
The Connectivity Map - cMap - Load signature :::
Information about your signature
::: Query Tab.
The Connectivity Map - cMap -
Query tab :::
Multiple Instance Query :::
The Connectivity Map - cMap - Results :::
::: Results Tab.
The Connectivity Map - cMap - Results :::
::: Results Tab.
+ scores
- scores
NULL scores
The Connectivity Map - cMap - Results formats :::
::: Results Tab.
Combined Results Agent (rather than an instance) focus
Permuted results Whole Perturbagen enrichment (set of instances) and p scores
Permutation p
The Connectivity Map - cMap - Scores & p-scores :::
::: Results Tab.
Down Score A high positive down score indicates that the corresponding perturbagen induced the expression of the probe sets in the down tag list. A high negative down score indicates that the corresponding perturbagen repressed the expression of the probe sets in the down tag list. The connectivity score is a combination of the up score and down score.
Up score: A value between +1 and -1 representing the absolute enrichment of a up tag list in a given instance. The up score is the “up” value reported on the result page. A high positive up score indicates that the corresponding perturbagen induced the expression of the probe sets in the up tag list. A high negative up score indicates that the corresponding perturbagen repressed the expression of the probe sets in the up tag list.
Permutation p: An estimate of the likelihood that the enrichment of a set of instances representing a specified perturbagen in the list of all instances in a given result would be observed by chance. This value is determined empirically by computing the enrichment of ten thousand sets of instances selected at random from the set of all instances in the result.
The Connectivity Map - cMap -
::: Results Tab.
Results tools :::
The Connectivity Map - cMap - Interpreting results :::
::: Results Tab.
Induce connection
Reverse connection
NO connection
The Connectivity Map - cMap -
Interpreting results :::
Strong Negative Connection
Signature - Perturbagen
Strong Positive Connection
Signature - Perturbagen
Some examples :::
Not clear connection Signature - Perturbagen
The Connectivity Map - cMap -
Interpreting results :::
Scores :::
High (positive or negative) connectivity scores and low p-scores are diserable.
However …
Strict adherence to p-scores is not recommended because they do not taken into account of the presence of null instances, instances of opposite sign or any instance attribute
The Connectivity Map - cMap -
Interpreting results :::
Running Sum Plot :::
Good separation of the two trajectories and maximum deviation from zero near opposite extremes of the x-axis is desirable when attempting to build confidence in particular hypotheses for challenging signatures. Alternatively, a minor peak at either end of the x-axis implies a strong affect on a portion of the signature. This may be sufficient evidence to call a hit for a complex signature, provided the effect is seen in multiple instances of the same perturbagens.
up tag file
down tag file
Walking--->
The Connectivity Map - cMap - Instances Tab :::
::: cMap Web Tool.
The Connectivity Map - cMap - Admin Tab :::
::: cMap Web Tool.