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A network biology approach to epigenetic regulation
Published on Jul 18, 20161119 Views
The description of molecular systems as networks opens the possibility of using all the methodology developed for network analysis in other fields from sociology to neurology. In this case, we have an
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Chapter list
1. Personalized Medicine 2.Epigenetics and Networks00:00
Core signaling pathways in human pancreatic cancers02:57
Identified as breast cancer susceptibility gene05:30
CNIO co-clinical cancer initiative - 107:28
Genomic alterations09:57
Case 3: High grade pancreatic neuroendocrine tumor - 113:42
Case 3: High grade pancreatic neuroendocrine tumor - 215:00
CNIO co-clinical cancer initiative - 216:40
Pancreas PDXs conserve key features of their tissue of origin - 117:21
Pancreas PDXs conserve key features of their tissue of origin - 218:47
CNIO co-clinical cancer initiative - 320:34
Science careers20:50
CNIO personalized Medicine Initiative23:46
CNIO co-clinical cancer initiative - 429:19
Clinical genetics has a big problem29:45
Bioinformatics for personalize medicine32:15
Alternative Splicing35:49
APPRIS - principal functional isoforms36:41
2 or more protein isoforms for 0.67% of the human genome37:50
Michael Tress48:31
Chimeras confirmed at the RNA and protein levels48:41
Transplicing/ chimeric mRNAs50:16
ChiTaRS: chimeric transcripts/proteins Database50:57
Technical Infrastructure52:21
Use cases are divided in:53:10
Bioinformatics Core Unit53:11
A Network Biology Approach to Information Processing in Epigenetic Regulation01:10:57
Complex relationship between Cytosine modifications01:11:01
Segmenting the Genome in Functional Regions01:14:16
20 Chromatin states01:15:24
Chromatin Related Proteins01:16:40
Epigenomic Mouse Stem Cell co-localization Network - 101:17:03
Epigenomic Mouse Stem Cell co-localization Network - 201:17:37
Inference of chromatin DIRECT co-localiztion networks from ChIP-seq data01:18:05
State 18 (Polycomb promoter)01:19:01
Global Co-localization network reflects organization in protein complexes01:19:53
Epigenetics as a communication system01:19:54
From “Location” to “Communication” Network01:20:35
Complexes01:20:59
Indegree (Transcription)01:22:14
Outdegree01:22:42
Co-localization network01:23:05
Influence/popularity01:23:28
Chromnets01:23:59
Overall enrichment of the chromatin states01:24:31
Histone modification or cytosine modification01:25:33
Co-evolution and evolutionary interactions01:25:39
Mirrortree Method: finding interaction partners at genome level01:25:45
Detecting co-evolving CrPs01:25:46
Getting a direct co-evolutionary network01:27:46
34 Co-evolution based connections of the 58 CrPs01:27:53
About metazoan co-evolution - 101:28:22
About metazoan co-evolution - 201:28:39
Co-evolution between 5hmC interactors01:28:41
5hmC key in communication & co-evolution in mESC01:28:43
Co-evolution Evolution of communication01:30:53
mESC Epigenetic Network (part 1)01:30:55
A network approach integrates 3D contacts with epigenomic data (part 2)01:31:16
Vera Pancaldi01:31:17
The 3D structure of chromatin01:31:46
Chromatin Interaction Networks (CINs)01:33:01
What about genes? PCHi-C!01:33:12
PCHi-C networks in mESCs - 101:33:31
PCHi-C networks in mESCs - 201:34:14
Chromatin Assortativity (ChAs)01:34:43
PCG is highly assortative in PCHi-C networks01:35:08
Chromatin Assortativity in different subnetworks01:35:51
Comparing P-P and P-O01:35:53
Assortativity of RNA Polymerase 201:35:56
Topological properties of PCG and RNAPII nodes01:36:01
Model proposed01:36:02
Experimental results on RNAPII S2p01:36:14
Epigenomic Mouse Stem Cell01:38:46
Looking for students, postdocs and bioinformaticians …01:39:40