2008 April | Indomitable Spirit

29-04-2008 Notes April 29

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Meeting with waterman

Discussed Wnt signaling pathway
Wnt is ligand, binds to receptor (Frizzled, 7-pass), activates cascading pathway
One part near the end of this are TCF family of DNA binding proteins, have C-terminal domain that binds beta-catenin (activator) as well as HMG-NLS domain
Beta-catenin accumulation → constitutively active TCFs → abberant regulation
Regulate (by activation at least) cell cycle proteins, what else?
Particular member of the family (TCF1) has extra DNA binding domain (other than HMG group that all in the family share) in E-tail (called C-clamp)
Does having C-clamp allow it to bind to other targets, or more strongly to some known targets?
For some reason, mutations show up first (often) in intestines/colon
Microarray performed by Waterman lab (unpublished) shows genes differentially expressed in cancer cells with different forms of TCF expressed (one normal, one missing beta-catenin domain), both with C-clamp
Look at expression difference, expect constitutively active version w/o B-cat domain to have genes increased in activity

2008-04-28 April 28

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Xiaohui’s class

Went over phastcons scoring method

One state models phylogenetic tree of conserved regions (with different states for codon position)

One state models non-conserved regions (multiple types of background

AIML talk

Discussion of modeling txn reaction, metabolic, etc. networks

Using machine learning (SVM, kernels) to get edges in the matrices

ODES governing these systems

Waterman project

Updated graph image generation in R of stats about motifs, genes

Downloaded PhastCons scores and RP scores for the new motif Nate described (more flexibility in 3′ end - instead of RCCG)

Generated stats images for original motifs

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29-04-2008 Notes April 29

2008-04-28 April 28