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Data Visualization Situation - Coggle Diagram
Data Visualization
Situation
Accessibility
Files
Github (Desktop)
Google Drive
not practical for continuous updates
better for archives
Communication
Twiitter
Instagram
Text
quick responses
not ideal for topics w/ substance
E-mail
great for topics w/ moderate substance
response time is moderate
Notes
Coda
not ideal for continuous note taking
good for archived notes
Questioning/Tasks
Questions (Mapping)
Consistency in cell volume
between cells?
YES: higher total molecule count show
the more active samples
NO: Dismiss
Retrieve thresholds (identifying significant concentration changes) of antibodies
Create filter for significant changes only.
Units of RPPA data
Refine graph labels
Identify expected molecules attached to
each pull-down protein
Filter noise for each pull-down
Find characteristics of data noise(s)
Lysate includes nucleus content?
Definition/Purpose of [antibody]_TOTAL label
Possible area for filtering and visualization of data
Clarification of phosphorylation site labeling
(does the mention of a phosphorylation site
mean it’s sensitive or insensitive to it)?
Is it possible to metastasize cancer cells in Petri dish?
Are the ERK pulled-down proteins from cytoplasm only?
Update the signal pathway
molecules’ origin documentation
Does PI3k p100 gamma antibody bind only when
attached to KRAS
Update signal pathway molecules’ origin documentation
Do the PP2A_alpha_subunit and PP2A_beta_subunit refer the beta and alpha isoforms in the catalytic subunit?
Is the BAD_112 antibody pick up only molecules
in the cytoplasm? Or the ones attached to EGFR as well?
What level is the rppa data ?
What pull down does ‘WT’ refer to?
Framework
Spatiotemporal Dependent Cytoplasm
Data Visualization
Pendings
Tumor cells seem to have a lack of 'Awareness'
Relevant t-SNE applications
Can t-SNE accurately cluster same antibodies between different samples?
Can t-SNE cluster same antibodies between different samples?
Can t-SNE de-noise data?
(use available categorization of molecules for comparison)
Auto-encoder application
Apply to experimental data
Look at PyCX for CAS model of cell automata
Off-topic t-SNE applications
Apply t-SNE (Word2Vec) to Cancer notes (name: Collaboration)
PCA applications
Perform different PCA forms
(e.g. kernel PCA)
Create Heat Map
PCA-ing data effectively groups molecules
as one functional unit or set
Create Heat Map
Rebuild ODE model of signal pathway
Linear combinations may have chaotic behavior (e.g. multiple MM equations)
Chaotic actions comes from inverse parabola models.
Inverse parabolas could be a linear combination of smaller elements (e.g. multiple MM equations)
Create flow diagram of signal pathway.
Use data to light up which molecules/parts of the signal pathway become activated.
Graph plots on log (just experimental value)