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| * [[/GSoC2010|Semantic Network Summary]] |
* [[GSoC2010_Directory|Semantic Network Summary Directory]] === Open Ideas And Links === * [[IdeaWall|Wall of Ideas (multi-project)]] * [[PapersToRead|Papers to read]] * [[ProjectLinks|Connectorium]] * [[ToDoNotes|To-do notes]] === Internal Exchanges === * [[Yeast_Chris|Yeast expression data (Chris)]] |
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| * '''Clinical Phenotype Ontology''' * Gianluca Colombo (UNIMIB - DISCo, Milano, Italy) |
* '''NF-Y (TF) targets: integrative analysis of ChIP-chip and transcript array data''' * Roberto Mantovani (UNIMI - DSBB, Milano, Italy) * '''Functional Landscape of p63 Transcription Factor Targets''' * Roberto Mantovani (UNIMI - DSBB, Milano, Italy) * Alessandro Terrinoni (Universita La Sapienza, Roma, Italy) |
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| * '''Functional Landscape of p63 Transcription Factor Targets''' * Roberto Mantovani (UNIMI - DSBB, Milano, Italy) * Alessandro Terrinoni (Universita La Sapienza, Roma, Italy) |
* '''Clinical Phenotype Ontology''' * Gianluca Colombo (UNIMIB - DISCo, Milano, Italy) == Educational == * [[attachment:CCBR_GeneExpressionLecture_2009_06.ppt|Overview of Microarray Data Analysis (CCBR graduate lecture)]] * [[attachment:MicroarrayAnalysis_Rprog_L4_v03.ppt|Microarray Analysis using R Part I: Exploratory Analysis (OBI course Summer 2010)]] * [[attachment:MicroarrayAnalysis_Rprog_L5_v03.ppt|Microarray Analysis using R Part II: Differential Expression (OBI course Summer 2010)]] * [[attachment:OBI_EnrPathwAnalysis_I_v13.ppt|Pathway Analysis (OBI course Spring 2010)]] Note: if you are interested in attending the full online version of these courses, please visit the [[http://ontariobiomedical.com/030~Courses/010~Bioinformatics_and_Genome_Analysis/|OBI web site]] |
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| * [[DanieleMerico/Code/Bioc2GMT|Generate gene set collections from Bioconductor libraries]] * [[DanieleMerico/Code/Read_GMT|Reads a GMT file into a R list object, or binary matrix]] |
==== Data Formatting ==== * gene sets * [[DanieleMerico/Code/Bioc2GMT|Generate gene set collections from Bioconductor libraries]] * [[DanieleMerico/Code/Read_GMT|Reads a GMT file into a R list object, or binary matrix]] * expression matrix * [[DanieleMerico/Code/Affy2GSEA|Convert Affy IDs to Entrez-Gene and add symbols and full names]] ==== Tests ==== * [[DanieleMerico/Code/Enr_FET|Fisher's Exact Test (with empirical FDR q-value included)]] |
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| === Network Visualization === * [[DanieleMerico/Code/NetworkGexpr_01|Format gene expression data and ppi interaction data for visualization in Cytoscape (OBI Course)]] |
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| == Educational Material == * [[attachment:CCBR_GeneExpressionLecture_2009_06.ppt|CCBR course on Microarray Data Analysis]] * [[attachment:OBI_EnrPathwAnalysis_I_v13.ppt|OBI course on Pathway Analysis]] |
== Public Data Resources == * [[GeneSetDB_02|Gene set collections]] == Online Supplementary Information == * Pinto et al, Nature 2010: [[Suppl/CNV_Pinto2010|Enrichment Test Code]] |
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| * is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is [[EdibleEnrichmentMaps|yes]] | * Is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is [[EdibleEnrichmentMaps|yes]] |
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| * Lorem ipsum. Opera sine nomine scripta * This is the Bader-lab, not the Baader-meinhof, if you had any doubt * It's a cruel yet marvelous world: * [[http://en.wikipedia.org/wiki/Ichneumonidae|Ichneumonidae]] * [[http://en.wikipedia.org/wiki/Emerald_cockroach_wasp|Emerald wasp]] * Indestructible life forms: * [[http://en.wikipedia.org/wiki/Tardigrades|Tardigrades]] * [[http://en.wikipedia.org/wiki/Cordyceps_unilateralis|Zombie Ants!]] |
Daniele Merico
Contact
Location: Common Lab Area, 6th Floor (CCBR)
Email: <daniele DOT merico AT gmail DOT com>
Skype: the-amerigo
Linked-In: Daniele Merico
Project Directory
Private Research Projects
Mouse Heart Disease Model Project (Transcriptomics, Proteomics, miRNA, Pathways)
- Functional Enrichment and Pathway Analysis in human genetics
Open Research Projects
- Google Summer of Code 2010
Open Ideas And Links
Internal Exchanges
Past Collaborations
NF-Y (TF) targets: integrative analysis of ChIP-chip and transcript array data
- Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
Functional Landscape of p63 Transcription Factor Targets
- Roberto Mantovani (UNIMI - DSBB, Milano, Italy)
- Alessandro Terrinoni (Universita La Sapienza, Roma, Italy)
Functional Landscape of RET Receptor Transcriptional Program
- Marco Antoniotti (UNIMIB - DISCo, Milano, Italy)
- Maria Grazia Borrello (Istituto Tumori - Milano, Italy)
- Gariboldi Manuela (Istituto Tumori / IFOM/IEO - Milano, Italy)
Clinical Phenotype Ontology
- Gianluca Colombo (UNIMIB - DISCo, Milano, Italy)
Educational
Overview of Microarray Data Analysis (CCBR graduate lecture)
Microarray Analysis using R Part I: Exploratory Analysis (OBI course Summer 2010)
Microarray Analysis using R Part II: Differential Expression (OBI course Summer 2010)
Note: if you are interested in attending the full online version of these courses, please visit the OBI web site
R Code Directory (Public)
Microarray Data Analysis
Gene-set Enrichment Analysis
Data Formatting
- gene sets
- expression matrix
Tests
ID Conversion
Network Visualization
Public Data Resources
Online Supplementary Information
Pinto et al, Nature 2010: Enrichment Test Code
CV and Publications
Trivia & Amenities
Is there a link holding together biology, computer science, mathematics, statistics and... coking? The answer is yes
How not to build an ontology: The Celestial Emporium of Benevolent Knowledge's Taxonomy
- Si Hoc Legere Scis Nimium Eruditionis Habes
- Datta. Dayadhvam. Damyata. Shantih shantih shantih.
- Lorem ipsum. Opera sine nomine scripta
- This is the Bader-lab, not the Baader-meinhof, if you had any doubt
- It's a cruel yet marvelous world:
- Indestructible life forms: