Data Visualization
Situation
Accessibility
Files
Communication
Twiitter
Github (Desktop)
Notes
Coda
Questions (Mapping)
Consistency in cell volume
between cells?
Retrieve thresholds (identifying significant concentration changes) of antibodies
YES: higher total molecule count show
the more active samples
NO: Dismiss
Create filter for significant changes only.
Units of RPPA data
Refine graph labels
Identify expected molecules attached to
each pull-down protein
Lysate includes nucleus content?
Filter noise for each pull-down
Find characteristics of data noise(s)
click to edit
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)?
click to edit
Is it possible to metastasize cancer cells in Petri dish?
click to edit
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?
click to edit
Is the BAD_112 antibody pick up only molecules
in the cytoplasm? Or the ones attached to EGFR as well?
click to edit
What level is the rppa data ?
click to edit
What pull down does ‘WT’ refer to?
click to edit
Framework
Spatiotemporal Dependent Cytoplasm
Data Visualization
Pendings
Tumor cells seem to have a lack of 'Awareness'
Relevant t-SNE applications
Auto-encoder application
Look at PyCX for CAS model of cell automata
Off-topic t-SNE applications
PCA applications
Rebuild ODE model of signal pathway
Linear combinations may have chaotic behavior (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)
Chaotic actions comes from inverse parabola models.
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)
Apply t-SNE (Word2Vec) to Cancer notes (name: Collaboration)
Apply to experimental data
Perform different PCA forms
(e.g. kernel PCA)
Inverse parabolas could be a linear combination of smaller elements (e.g. multiple MM equations)
Create Heat Map
PCA-ing data effectively groups molecules
as one functional unit or set
Create Heat Map
Google Drive
Text
click to edit
not practical for continuous updates
better for archives
not ideal for continuous note taking
good for archived notes
Questioning/Tasks
click to edit
quick responses
not ideal for topics w/ substance
click to edit
click to edit
great for topics w/ moderate substance
response time is moderate