|
Size: 1122
Comment:
|
← Revision 15 as of 2011-10-31 19:40:41 ⇥
Size: 3844
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 6: | Line 6: |
| ''The human genome and drug discovery after a decade. Roads (still) not taken'' | [[http://arxiv.org/abs/1102.0448|''The human genome and drug discovery after a decade. Roads (still) not taken'']] |
| Line 8: | Line 8: |
| Ruth Isserlin 1 ,Stephen Frye 2, Timothy Willson 3, Frank H. Yu 4, Gary D. Bader 1 *, Aled Edwards 5 * | Ruth Isserlin 1, Gary D. Bader 1 *, Aled Edwards 2 * ,Stephen Frye 3, Timothy Willson 4, Frank H. Yu 5 |
| Line 11: | Line 11: |
| 1. University of Toronto, Toronto, Ontario Canada, M5G 1L7 | |
| Line 14: | Line 15: |
| 1. University of Toronto, Toronto, Ontario Canada, M5G 1L7 | Also, see [[http://www.ncbi.nlm.nih.gov/pubmed/21307913|Too many roads not taken]], a companion paper published in Nature. 2011 Feb 10;470(7333):163-5 |
| Line 18: | Line 20: |
| * [[attachment:query_pubmed.pl]] * Example input files: * list of gene ids to be searched in pubmed - [[attachment:geneids.txt]] * list of terms to exclude from the queries - [[attachment:exclusionlist.txt]] |
|
| Line 20: | Line 26: |
| [[attachment:SupplementaryFigure1_highqualityProbes.pdf]]<<BR>> '''Supplementary Figure 1: NR Growth curves with high quality probes'''<<BR>> Individual Citation Growth curves for each Nuclear Hormone Receptor that has a high quality chemical tool associated with it. The growth at one year is shown relative to the previous year. Citation growth is calculated for each time frame by taking the normalized citation count from the previous time frame and subtracting it from the current normalized citation count. Citation counts are normalized to the total number of citations for the entire NR group for the given time frame. The formula is ((|nc2 - nc1|)/nc1) * 100, where nc1 is the fraction of citations for a given gene in year n compared to all citations for the gene family and nc2 is the fraction of citations for a given gene in year n+1. Graphs are annotated with year of probe publication and the year the receptor was cloned. [[attachment:SupplementaryFigure2_unpublishedProbes.pdf]]<<BR>> '''Supplementary Figure 2: NR Growth curves with unpublished or restricted probes'''<<BR>> Individual Citation Growth curves for each Nuclear Hormone Receptor that has a probe but the probe might be unpublished, restricting it use. [[attachment:SupplementaryFigure3_noProbes.pdf]]<<BR>> '''Supplementary Figure 3: NR Growth curves with no probes'''<<BR>> Individual Citation Growth curves for each Nuclear Hormone Receptor that does not have a probe. == Supplementary Tables == == High Resolution Figures == [[attachment:figure1_NR_19502009.pdf]]<<BR>> '''Figure 1: Human NR Citations (1950-2009)''' [[attachment:figure2_kinases_19502009.pdf]]<<BR>> '''Figure 2: Human Protein Kinase Publications 1950-2009''' [[attachment:figure3_NR_19501995_vs2009.pdf]]<<BR>> '''Figure 3: Human NR Citations 1950-1995 vs. 2009''' [[attachment:figure4_NR_2009_probes.pdf]]<<BR>> '''Figure 4: Chemical Tools associated with Human Nuclear Hormone Receptors''' [[attachment:figure5_Ionchannels_19502009_vs2009.pdf]]<<BR>> '''Figure 5: Ion Channel Citations 1950-2000 vs. 2009''' == Original PubMed Query Results == 1. [[attachment:NuclearHormoneReceptors.xlsx]] 1. [[attachment:Kinases.xlsx]] 1. [[attachment:IonChannels.xlsx]] 1. [[attachment:MethylTransferases.xls]] |
The human genome and drug discovery after a decade. Roads (still) not taken
This data is supplementary material for:
''The human genome and drug discovery after a decade. Roads (still) not taken''
Ruth Isserlin 1, Gary D. Bader 1 *, Aled Edwards 2 * ,Stephen Frye 3, Timothy Willson 4, Frank H. Yu 5
- Donnelly Centre for Cellular and Biomolecular Research, Faculty of Medicine, University of Toronto, 160 College Street, Toronto, Ontario, Canada M5S 3E1
- University of Toronto, Toronto, Ontario Canada, M5G 1L7
- Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA 27599
GlaxoSmithKline, Research Triangle Park, North Caroline, USA 27709
- Neurobiology and Dental Research Institute, School of Dentistry, Seoul National University, Seoul, South Korea, 110-749
Also, see Too many roads not taken, a companion paper published in Nature. 2011 Feb 10;470(7333):163-5
Code
- If you are interested in seeing the citations for your set of genes please use the following script to query pubmed with your genes of interest.
- Example input files:
list of gene ids to be searched in pubmed - geneids.txt
list of terms to exclude from the queries - exclusionlist.txt
Supplementary Figures
SupplementaryFigure1_highqualityProbes.pdf
Supplementary Figure 1: NR Growth curves with high quality probes
Individual Citation Growth curves for each Nuclear Hormone Receptor that has a high quality chemical tool associated with it. The growth at one year is shown relative to the previous year. Citation growth is calculated for each time frame by taking the normalized citation count from the previous time frame and subtracting it from the current normalized citation count. Citation counts are normalized to the total number of citations for the entire NR group for the given time frame. The formula is ((|nc2 - nc1|)/nc1) * 100, where nc1 is the fraction of citations for a given gene in year n compared to all citations for the gene family and nc2 is the fraction of citations for a given gene in year n+1. Graphs are annotated with year of probe publication and the year the receptor was cloned.
SupplementaryFigure2_unpublishedProbes.pdf
Supplementary Figure 2: NR Growth curves with unpublished or restricted probes
Individual Citation Growth curves for each Nuclear Hormone Receptor that has a probe but the probe might be unpublished, restricting it use.
SupplementaryFigure3_noProbes.pdf
Supplementary Figure 3: NR Growth curves with no probes
Individual Citation Growth curves for each Nuclear Hormone Receptor that does not have a probe.
Supplementary Tables
High Resolution Figures
figure1_NR_19502009.pdf
Figure 1: Human NR Citations (1950-2009)
figure2_kinases_19502009.pdf
Figure 2: Human Protein Kinase Publications 1950-2009
figure3_NR_19501995_vs2009.pdf
Figure 3: Human NR Citations 1950-1995 vs. 2009
figure4_NR_2009_probes.pdf
Figure 4: Chemical Tools associated with Human Nuclear Hormone Receptors
figure5_Ionchannels_19502009_vs2009.pdf
Figure 5: Ion Channel Citations 1950-2000 vs. 2009