We recently generated tissue and cancer specific biological networks and presented here in TCSBN (a database of tissue and cancer specific biological networks). This database is run by Sysmedicine group, SciLifeLab, KTH, Sweden, as part of recent our studies (please see citation below).
This database contains co-expression networks for 46 normal tissues and 17 cancers, and integrated networks (i.e. protein interaction network and transcriptional regulatory network) of three tissues, liver, muscle and adipose tissue. Here users can explore the functionally or physically associated proteins from given networks and test their biological hypothesis and develop efficient treatment strategies.
We wish that our database will greatly benefit research community in biology and medicine.
To those who consider to use our database, please cite papers below:
- 1. Database: Sunjae Lee#, Cheng Zhang#, Muhammad Arif#, Rui Benfeitas, Gholamreza Bidkhori, Zhengtao Liu, Rui Benfetias, Gholamreza Bidkhori, Sumit Deshmukh, Mohamed Al Shobky, Alen Lovric, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu, (2017), TCSBN: a database of tissue and cancer specific biological networks, Nucleic Acids Research LINK TO JOURNAL
- 2. Integrated networks: Sunjae Lee#, Cheng Zhang#, Murat Kilicarslan#, Brian D. Piening, Elias Björnson, Björn M. Hallstrom, Albert K. Groen, Ele Ferrannini, Markku Laakso, Michael Snyder, Matthias Blűher, Mathias Uhlen, Jens Nielsen, Ulf Smith, Mireille J. Serlie, Jan Boren, Adil Mardinoglu, (2016), Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance, Cell Metabolism LINK TO JOURNAL
- 3. Human tissue co-expression networks: Sunjae Lee#, Cheng Zhang#, Zhengtao Liu#, Martina Klevstig, Bani Mukhopadhyay, Mattias Bergentall, Resat Cinar, Marcus Ståhlman, Natasha Sikanic, Joshua K. Park, Sumit Deshmukh, Azadeh M. Pour, Tim Kuijpers, Morten Grøtli, Simon J. Elsässer, Brian D. Piening, Michael Snyder, Jens Nielsen, Fredrik Bäckhed, George Kunos, Mathias Uhlen, Jan Boren, Adil Mardinoglu, (2017), Network analyses identify liver-specific targets for treating liver diseases, Molecular Systems Biology LINK TO JOURNAL
- 4. Cancer co-expression networks: Mathias Uhlen, Cheng Zhang, Sunjae Lee, Evelina Sjöstedt, Linn Fagerberg, Gholamreza Bidkhori, Rui Benfeitas, Muhammad Arif, Zhengtao Liu, Fredrik Edfors, Kemal Sanli, Kalle von Feilitzen, Per Oksvold, Emma Lundberg, Sophia Hober, Peter Nilsson, Johanna Mattsson, Jochen M. Schwenk, Hans Brunnström, Bengt Glimelius, Tobias Sjöblom, Per-Henrik Edqvist, Dijana Djureinovic, Patrick Micke, Cecilia Lindskog, Adil Mardinoglu#, Fredrik Ponten#, (2017), A pathology atlas of the human cancer transcriptome, Science LINK TO JOURNAL
Please contact Sunjae Lee (firstname.lastname@example.org) for further details.
1. Full edge table for cancer co-expression networks
2. Full edge table for normal tissue co-expression networks
3. Full edge table for integrated networks
4. Annotation table for network category
1. Bug Fixed on directionality for co-expression network (11-09-2017)
2. Edge table added (12-09-2017)
3. Updated Edge Query: sorted by absolute correlation values (13-09-2017)
4. P-value added (14-09-2017)
5. Edge pruning parameter added (15-09-2017)
6. Changed mouse action on edges to show correlation (mouse-over to left-click) (25-10-2017)