ArrayExpress Uploader0mouseInduced macrophagesnot specifiedInduced macrophagesnot specifiedInduced macrophagesnot specifiedInduced macrophagesnot specifiedInduced macrophagesnot specifiedInduced macrophagesnot specifiedIndependent iHep cell linenot specifiedIndependent iHep cell linenot specifiedIndependent iHep cell linenot specifiedliverE14.5liverE14.5liver8-week-old adultliver8-week-old adultiHepsnot specifiediHepsnot specifiedcolon8-week-old adultcolon8-week-old adultiHepsnot specifiediHepsnot specifiediHepsnot specifiediHepsnot specifiediHepsnot specifiediHepsnot specifiediHepsnot specifiediHepsnot specified7670arrayexpress_sid6Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully...E-GEOD-59037/profile/8773/arrayexpressuploader225cellcolonendodermintestinal epitheliummacrophageDec.12, 2014Falsedissecting-engineered-cell-types-and-enhancing-celE-GEOD-59037_A-AFFY-45Dissecting engineered cell types and enhancing cell fate conversion via CellNetNov.12, 2014Engineering clinically relevant cells in vitro holds promise for regenerative medicine, but most protocols fail to faithfully recapitulate target cell properties. To address this, we developed CellNet, a network biology platform that determines whether engineered cells are equivalent to their target tissues, diagnoses aberrant gene regulatory networks, and prioritizes candidate transcriptional regulators to enhance engineered conversions. Using CellNet, we improved B cell to macrophage conversion, transcriptionally and functionally, by knocking down predicted B cell regulators. Analyzing conversion of fibroblasts to induced hepatocytes (iHeps), CellNet revealed an unexpected intestinal program regulated by the master regulator Cdx2. We observed functional engraftment of mouse colon by iHeps, thereby establishing their broader potential as endoderm progenitors and demonstrating direct conversion of fibroblasts into intestinal epithelium. Our studies illustrate how CellNet can be employed to improve direct conversion and to uncover unappreciated properties of engineered cells. 15 sampleshttp://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-59037http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-59037/samples/