This database and web-site are no longer maintained. Our updated stem cell integarted database that contains all datasets from here and more can be found at:


Integrated Stem Cell Molecular Interaction Database (iScMiD) is an initial database for disseminating and displaying gene regulatory networks in stem cells. It currently contains interactions from 12 recent publications of profiling stem-cell related transcription factors using various high throughput ChIP profiling methods. The resultant integrated network has 50,250 entries. The network can be downloaded from here. The file contains four columns: transcription factor (TF), target gene, PubMed ID (pmid), and organism (mouse/human). Please be aware that this network is likely to contain many false-positives and should be used for hypothesis generation only.

Using a seed list of 264 genes known to play a role in stem-cell self renewal, differentiation and the cell cycle we constructed a subnetwork that only connects those genes. This network has 1739 links and 264 nodes and can be downloaded in sig format for analysis and visualization with SNAVI, sif format for analysis and visualization with Cytoscape and tgf format for analysis and visualization with yEd formats. Users can also browse (best viewed with Internet Explorer and requires Adobe SVG Viewer) nodes within this network where links to references and graphical connectivity diagrams are provided.

Core20 is an additional smaller subnetwork that contains 156 directed interactions among the 20 core transcription factors used as baits in the ChIP experiments. This subnetwork can be visualized here, and downloaded in csv, sig, sif and tgf formats.


Literature-based ES Network

Literature-based stem-cell network is a regulatory network extracted by Hulei Xu from low-throughput studies reported in the stem-cell literature. The network is created by combining data from 271 publications and contains cell-signaling and gene-regulatory links that can be direct or indirect. The network can be browsed and downloaded from here.


Other related subnetwork

Nanog-interactome is a protein-protein interaction network created using a serial set of AP/MS experiments. This network was published in 2006 by Jianlong Wang et al. Nature 444:364-8 (2006) PMID: 17093407. This network has also been visualized. This network can be downloaded in sig, sif, tgf, Pajek net and BioPAX formats.