Methods for diagnosis, prognosis and treatment

A method comprising:

• obtaining primary cells from an individual, the cells are associated with cancer or autoimmune disease;
• determining activation state data for phosphorylated proteins within single cells from the individual by a process comprising:
• contacting the cells with at least two modulators;
• contacting the cells with a plurality of binding elements;
• detecting the binding elements on a single cell basis using a flow cytometer;
• identifying cell pathways and signaling pathway disruptions using the activation state data;
• determining a clinical outcome for the individual by comparing the activation state data to a database containing activation state data linked to clinical information from other individuals and when therapeutic action was taken or not taken;
• matching the clinical outcome of the individual to biological profiles that guide the selection of therapeutic regimens,
• generating a report containing the activation state data, diagnosis or treatment information, cell characterization information, signaling responses to modulators, apoptosis inducing agents and drug response readouts, using a computer;
• accessing or transmitting the report over the internet, a web portal or network by a third party or to a third party;
• providing therapeutic treatment based on the activation state data of the single cells;
• and
• adding the activation state data to the database containing activation state data linked to clinical information.