Tip of the Week: ENCODE data in the UCSC Genome Browser

Usually our “tip of the week” posts are a ~5 minute movie of some interesting site or software feature that we come across. But this week’s tip is different. It’s somewhat longer. But we think it’s data that you should know about–because every time we show this to people in workshops or at our booth at ASHG people are really psyched to find out about it. Learn about the ENCODE data that is stored and displayed in the UCSC Genome Browser in this tutorial, which is being made freely available because the UCSC team worked with us and sponsored us to create this.

The ENCODE project’s goal is:

to build a comprehensive parts list of the functional elements of the human genome, including elements that act at the protein level (coding genes) and RNA level (non-coding genes), and regulatory elements that control the cells and circumstances in which a gene is active.

The genome sequence data was great–but it wasn’t enough. The ENCODE folks are already generating tremendous amounts of data toward these aims. This tutorial provides background on the ENCODE project, and guidance on new data. It began as a pilot project looking at just 1% of the genome, but has now matured into an active genome-wide production phase effort that is yielding fascinating information that you might want to know about. Is there evidence of certain transcription factor binding upstream of your favorite gene? It might be in there now. Find the Yale TFBS track, or the HAIB TFBS track, turn it on if it’s not by default, and have a look. Interested in possible enhancers? How about transcription levels? Check out the new super-track that can display that data.  There’s plenty more data as well. Did you know that different cell lines are showing evidence of CNVs? We’ll show you how to identify the ENCODE data sets and begin to explore them.

As I’ve mentioned before, the data is not in publications at this point–and it may never be in the formal way. You are going to have to investigate this yourself. We can point you in the right direction, and hand you the map. And then you can have some fun orienteering around the genome.

Tutorial access directly: http://www.openhelix.com/ENCODE


Pilot project for background: Birney, E., Stamatoyannopoulos, J., Dutta, A., Guigó, R., Gingeras, T., Margulies, E., Weng, Z., Snyder, M., Dermitzakis, E., Stamatoyannopoulos, J., Thurman, R., Kuehn, M., Taylor, C., Neph, S., Koch, C., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J., Andrews, R., Flicek, P., Boyle, P., Cao, H., Carter, N., Clelland, G., Davis, S., Day, N., Dhami, P., Dillon, S., Dorschner, M., Fiegler, H., Giresi, P., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K., Johnson, B., Johnson, E., Frum, T., Rosenzweig, E., Karnani, N., Lee, K., Lefebvre, G., Navas, P., Neri, F., Parker, S., Sabo, P., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu1, M., Collins, F., Dekker, J., Lieb, J., Tullius, T., Crawford, G., Sunyaev, S., Noble, W., Dunham, I., Dutta, A., Guigó, R., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I., Baertsch, R., Keefe, D., Flicek, P., Dike, S., Cheng, J., Hirsch, H., Sekinger, E., Lagarde, J., Abril, J., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M., Thomas, D., Weirauch, M., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K., Sung, W., Ooi, H., Chiu, K., Foissac, S., Alioto, T., Brent, M., Pachter, L., Tress, M., Valencia, A., Choo, S., Choo, C., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T., Brown, J., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Henrichsen, C., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J., Carninci, P., Hayashizaki, Y., Weissman, S., Dermitzakis, E., Margulies, E., Hubbard, T., Myers, R., Rogers, J., Stadler, P., Lowe, T., Wei, C., Ruan, Y., Snyder, M., Birney, E., Struhl, K., Gerstein, M., Antonarakis, S., Gingeras, T., Brown, J., Flicek, P., Fu, Y., Keefe, D., Birney, E., Denoeud, F., Gerstein, M., Green, E., Kapranov, P., Karaöz, U., Myers, R., Noble, W., Reymond, A., Rozowsky, J., Struhl, K., Siepel, A., Stamatoyannopoulos, J., Taylor, C., Taylor, J., Thurman, R., Tullius, T., Washietl, S., Zheng, D., Liefer, L., Wetterstrand, K., Good, P., Feingold, E., Guyer, M., Collins, F., Margulies, E., Cooper, G., Asimenos, G., Thomas, D., Dewey, C., Siepel, A., Birney, E., Keefe, D., Hou, M., Taylor, J., Nikolaev, S., Montoya-Burgos, J., Löytynoja, A., Whelan, S., Pardi, F., Massingham, T., Brown, J., Huang, H., Zhang, N., Bickel, P., Holmes, I., Mullikin, J., Ureta-Vidal, A., Paten, B., Seringhaus, M., Church, D., Rosenbloom, K., Kent, W., Stone, E., Sequencing Program*, N., Human Genome Sequencing Center*, B., Genome Sequencing Center*, W., Broad Institute*, ., Oakland Research Institute*, C., Gerstein, M., Antonarakis, S., Batzoglou, S., Goldman, N., Hardison, R., Haussler, D., Miller, W., Pachter, L., Green, E., Sidow, A., Weng, Z., Trinklein, N., Fu, Y., Zhang, Z., Karaöz, U., Barrera, L., Stuart, R., Zheng, D., Ghosh, S., Flicek, P., King, D., Taylor, J., Ameur, A., Enroth, S., Bieda, M., Koch, C., Hirsch, H., Wei, C., Cheng, J., Kim, J., Bhinge, A., Giresi, P., Jiang, N., Liu, J., Yao, F., Sung, W., Chiu, K., Vega, V., Lee, C., Ng, P., Shahab, A., Sekinger, E., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M., Inman, D., Singer, M., Richmond, T., Munn, K., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Clelland, G., Wilcox, S., Dillon, S., Andrews, R., Fowler, J., Couttet, P., James, K., Lefebvre, G., Bruce, A., Dovey, O., Ellis, P., Dhami, P., Langford, C., Carter, N., Vetrie, D., Kapranov, P., Nix, D., Bell, I., Patel, S., Rozowsky, J., Euskirchen, G., Hartman, S., Lian, J., Wu, J., Urban, A., Kraus, P., Van Calcar, S., Heintzman, N., Hoon Kim, T., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C., Rosenfeld, M., Aldred, S., Cooper, S., Halees, A., Lin, J., Shulha, H., Zhang, X., Xu, M., Haidar, J., Yu, Y., Birney*, E., Weissman, S., Ruan, Y., Lieb, J., Iyer, V., Green, R., Gingeras, T., Wadelius, C., Dunham, I., Struhl, K., Hardison, R., Gerstein, M., Farnham, P., Myers, R., Ren, B., Snyder, M., Thomas, D., Rosenbloom, K., Harte, R., Hinrichs, A., Trumbower, H., Clawson, H., Hillman-Jackson, J., Zweig, A., Smith, K., Thakkapallayil, A., Barber, G., Kuhn, R., Karolchik, D., Haussler, D., Kent, W., Dermitzakis, E., Armengol, L., Bird, C., Clark, T., Cooper, G., de Bakker, P., Kern, A., Lopez-Bigas, N., Martin, J., Stranger, B., Thomas, D., Woodroffe, A., Batzoglou, S., Davydov, E., Dimas, A., Eyras, E., Hallgrímsdóttir, I., Hardison, R., Huppert, J., Sidow, A., Taylor, J., Trumbower, H., Zody, M., Guigó, R., Mullikin, J., Abecasis, G., Estivill, X., Birney, E., Bouffard, G., Guan, X., Hansen, N., Idol, J., Maduro, V., Maskeri, B., McDowell, J., Park, M., Thomas, P., Young, A., Blakesley, R., Muzny, D., Sodergren, E., Wheeler, D., Worley, K., Jiang, H., Weinstock, G., Gibbs, R., Graves, T., Fulton, R., Mardis, E., Wilson, R., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D., Chang, J., Lindblad-Toh, K., Lander, E., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshinaga, Y., Zhu, B., & de Jong, P. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature, 447 (7146), 799-816 DOI: 10.1038/nature05874

Rosenbloom, K., Dreszer, T., Pheasant, M., Barber, G., Meyer, L., Pohl, A., Raney, B., Wang, T., Hinrichs, A., Zweig, A., Fujita, P., Learned, K., Rhead, B., Smith, K., Kuhn, R., Karolchik, D., Haussler, D., & Kent, W. (2009). ENCODE whole-genome data in the UCSC Genome Browser Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp961

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