Protein-DNA interactions

Human Protein-DNA Interactome (hPDI)

The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The current release of hPDI contains 17,718 protein-DNA interactions for 1013 human DNA-binding proteins. These DNA-binding proteins include 493 human transcription factors (TFs) and 520 unconventional DNA binding proteins (uDBPs). Here TFs are defined as proteins either are annotated as "regulation of transcription" defined by GO database or contain known DNA binding domains defined by Pfam database and, uDBPs are defined proteins that have not been previously found to binding DNA specifically.

Click here for frequently asked questions.

 Protein View

Input a human protein ID (e.g.USF1, ERK2):

 Motif Search

Input a segment of DNA sequence and find which proteins (TF or uDBP) might bind to it:
[sequence format: only the DNA sequence; not FASTA format]

 Class View

Select a class of proteins and obtain a summary table of the proteins:


Download bulk files



Xie, Z., Hu, S.H., Blackshaw, S., Zhu, H. and Qian, J. (2009) hPDI: a database of experimental human protein-DNA interactions, Bioinformatics. (In press)

Hu, S.H., Xie, Z., Onishi, A., Yu, X.P., Jiang, L.Z., Lin, J., Rho, H.S., Woodard, C., Wang, H., Jeong, J.S., Long, S.Y., He, X.F., Blackshaw, S., Qian, Q. and Zhu, H. (2009) Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signalling, Cell, 139, 610-622.

Maintained by Dr. Jiang Qian and Dr. Zhi Xie at the Qian's Bioinformatics Lab, Johns Hopkins School of Medicine