From 3b2f3e2d488fdb157904a8f1d3e8958d12a92dc9 Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Tue, 28 Feb 2017 18:30:04 +0000 Subject: [PATCH 1/7] Revert code to be compatible with v1.2 DB schema --- eForge/eForge.pm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index fb16d05..165c740 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -481,10 +481,9 @@ sub proximity_filter { my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1; $end = @$probe_ids - 1 if ($end >= @$probe_ids); - my $sql = "SELECT probe_id, proxy_probes FROM proxy_filter JOIN array USING (array_id) WHERE". - " array_tag = ? AND probe_id IN (?". (",?" x ($end - $start)).")"; + my $sql = "SELECT probe_id, proxy_probes FROM proxy_filter WHERE probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare($sql); #get the blocks form the ld table - $sth->execute($array_tag, @$probe_ids[$start..$end]); + $sth->execute(@$probe_ids[$start..$end]); my $result = $sth->fetchall_arrayref(); $sth->finish(); From fdad87d3bc8ea4287c7bf9199badabac486d2650 Mon Sep 17 00:00:00 2001 From: charlesbreeze Date: Wed, 30 Nov 2016 14:49:02 +0000 Subject: [PATCH 2/7] Update index.pl --- webserver/cgi-bin/index.pl | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index bd9893d..5daaf21 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -811,9 +811,11 @@ =head2 print_credits_box sub print_credits_box { print Template::content_box("Credits", - "Breeze CE, Paul DS, Butcher LM, Herrero J, Birney E, Dunham I, Beck S. eFORGE: A tool for - identifying tissue-specific signal in epigenomic data. Manuscript in preparation. -
", + "Breeze, C.E.*, Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., + Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., + Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., + Birney, E., Dunham, I., Beck, S.*, 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. + Cell Reports 17, 2137–2150. doi:10.1016/j.celrep.2016.10.059
", ); } From 48c0719cbc34f679fe3db9ecd3d7a8768daf684e Mon Sep 17 00:00:00 2001 From: charlesbreeze Date: Wed, 30 Nov 2016 14:54:08 +0000 Subject: [PATCH 3/7] Update index.pl --- webserver/cgi-bin/index.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 5daaf21..ddcb144 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -811,10 +811,10 @@ =head2 print_credits_box sub print_credits_box { print Template::content_box("Credits", - "Breeze, C.E.*, Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., + "Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., - Birney, E., Dunham, I., Beck, S.*, 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. + Birney, E., Dunham, I., Beck, S., 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17, 2137–2150. doi:10.1016/j.celrep.2016.10.059
", ); } From 9a01a5c16996c06b80d23463ff5a7a20c3efbace Mon Sep 17 00:00:00 2001 From: charlesbreeze Date: Wed, 30 Nov 2016 15:37:22 +0000 Subject: [PATCH 4/7] Update index.pl --- webserver/cgi-bin/index.pl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index ddcb144..0a6da07 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -1129,6 +1129,17 @@ sub print_about_page { Stephan Beck: s.beck(at)ucl.ac.uk.", ); + + print Template::content_box("Some of the papers that cite eFORGE", + "eFORGE application and methodology is described at length in the following article:", + "Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., Birney, E., Dunham, I., Beck, S., 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17, 2137–2150. doi:10.1016/j.celrep.2016.10.059 ", + "In addition, as of 30th of November 2016, eFORGE has either been referenced or applied by the following publications (for an updated list of references, see Google Scholar ):", + "Stunnenberg, H.G., Abrignani, S., Adams, D., Almeida, M. de, Altucci, L., Amin, V., Amit, I., Antonarakis, S.E., Aparicio, S., Arima, T., Arrigoni, L., Arts, R., Asnafi, V., Badosa, M.E., Bae, J.-B., Bassler, K., Beck, S., Berkman, B., Bernstein, B.E., Bilenky, M., Bird, A., Bock, C., Boehm, B., Bourque, G., Breeze, C.E., et al. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell 167, 1145–1149", + "Spurrell, C.H., Dickel, D.E., Visel, A., 2016. The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell167, 1163-1166. doi:10.1016/j.cell.2016.10.054", + "Lewis, J., Breeze, C.E., Charlesworth, J., Maclaren, O.J., and Cooper, J. (2016). Where next for the reproducibility agenda in computational biology? BMC Syst. Biol. 10, 52", + "Bartlett, T.E., Chindera, K., McDermott, J., Breeze, C.E., Cooke, W.R., Jones, A., Reisel, D., Karegodar, S.T., Arora, R., Beck, S., et al. (2016). Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat. Commun. 7, 11620.", + "van Dongen, J., Nivard, M.G., Willemsen, G., Hottenga, J.-J., Helmer, Q., Dolan, C.V., Ehli, E.A., Davies, G.E., van Iterson, M., Breeze, C.E., Beck, S., et al. (2016). Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun. 7, 11115.",); + print_credits_box(); print Template::end; exit(0); From 3f651020f59ee183ca54b65d0a0e0c575e6abebd Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Tue, 28 Feb 2017 18:46:59 +0000 Subject: [PATCH 5/7] Fix reference pages and DOI URL --- webserver/cgi-bin/index.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 0a6da07..98e083c 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -815,7 +815,7 @@ sub print_credits_box { Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., Birney, E., Dunham, I., Beck, S., 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. - Cell Reports 17, 2137–2150. doi:10.1016/j.celrep.2016.10.059
", + Cell Reports 17, 2137-2150. http://dx.doi.org/10.1016/j.celrep.2016.10.059
", ); } From 6c9c95d260f5cdfbc9211420018d65fb5e36b89e Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Wed, 1 Mar 2017 16:05:38 +0000 Subject: [PATCH 6/7] Fix the references --- webserver/cgi-bin/index.pl | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 98e083c..db73d62 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -811,11 +811,7 @@ =head2 print_credits_box sub print_credits_box { print Template::content_box("Credits", - "Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., - Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., - Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., - Birney, E., Dunham, I., Beck, S., 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. - Cell Reports 17, 2137-2150. http://dx.doi.org/10.1016/j.celrep.2016.10.059
", + "Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S (2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059
", ); } @@ -1132,13 +1128,13 @@ sub print_about_page { print Template::content_box("Some of the papers that cite eFORGE", "eFORGE application and methodology is described at length in the following article:", - "Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.-É., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H.G., Teschendorff, A.E., Herrero, J., Birney, E., Dunham, I., Beck, S., 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17, 2137–2150. doi:10.1016/j.celrep.2016.10.059 ", + "Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S (2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059", "In addition, as of 30th of November 2016, eFORGE has either been referenced or applied by the following publications (for an updated list of references, see Google Scholar ):", - "Stunnenberg, H.G., Abrignani, S., Adams, D., Almeida, M. de, Altucci, L., Amin, V., Amit, I., Antonarakis, S.E., Aparicio, S., Arima, T., Arrigoni, L., Arts, R., Asnafi, V., Badosa, M.E., Bae, J.-B., Bassler, K., Beck, S., Berkman, B., Bernstein, B.E., Bilenky, M., Bird, A., Bock, C., Boehm, B., Bourque, G., Breeze, C.E., et al. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell 167, 1145–1149", - "Spurrell, C.H., Dickel, D.E., Visel, A., 2016. The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell167, 1163-1166. doi:10.1016/j.cell.2016.10.054", - "Lewis, J., Breeze, C.E., Charlesworth, J., Maclaren, O.J., and Cooper, J. (2016). Where next for the reproducibility agenda in computational biology? BMC Syst. Biol. 10, 52", - "Bartlett, T.E., Chindera, K., McDermott, J., Breeze, C.E., Cooke, W.R., Jones, A., Reisel, D., Karegodar, S.T., Arora, R., Beck, S., et al. (2016). Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat. Commun. 7, 11620.", - "van Dongen, J., Nivard, M.G., Willemsen, G., Hottenga, J.-J., Helmer, Q., Dolan, C.V., Ehli, E.A., Davies, G.E., van Iterson, M., Breeze, C.E., Beck, S., et al. (2016). Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun. 7, 11115.",); + "Stunnenberg HG; International Human Epigenome Consortium., Hirst M. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 17;167(5):1145-1149. doi: 10.1016/j.cell.2016.11.007", + "Spurrell CH, Dickel DE, Visel A. (2016). The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell 167(5):1163-1166. doi: 10.1016/j.cell.2016.10.054. Review", + "Lewis J, Breeze CE, Charlesworth J, Maclaren OJ, Cooper J. (2016). Where next for the reproducibility agenda in computational biology? BMC Syst. Biol. 10(1):52 doi: 10.1186/s12918-016-0288-x", + "Bartlett TE, Chindera K, McDermott J, Breeze CE, Cooke WR, Jones A, Reisel D, Karegodar ST, Arora R, Beck S, Menon U, Dubeau L, Widschwendter M. (2016). Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat. Commun. 7:11620. doi: 10.1038/ncomms11620", + "van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S; BIOS Consortium., Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI. (2016). Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun. 7:11115. doi: 10.1038/ncomms11115"); print_credits_box(); print Template::end; From e37c574e35ebf1fc58991cf65435f73243a9ce45 Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Fri, 3 Mar 2017 11:53:44 +0000 Subject: [PATCH 7/7] More updates on the list of papers that cite eFORGE --- webserver/cgi-bin/index.pl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index db73d62..fc7be3a 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -1129,9 +1129,15 @@ sub print_about_page { print Template::content_box("Some of the papers that cite eFORGE", "eFORGE application and methodology is described at length in the following article:", "Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S (2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports 17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059", - "In addition, as of 30th of November 2016, eFORGE has either been referenced or applied by the following publications (for an updated list of references, see Google Scholar ):", + "In addition, as of 27th of February 2017, eFORGE has either been referenced or applied by the following publications (for an updated list of references, see Google Scholar):", "Stunnenberg HG; International Human Epigenome Consortium., Hirst M. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 17;167(5):1145-1149. doi: 10.1016/j.cell.2016.11.007", "Spurrell CH, Dickel DE, Visel A. (2016). The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell 167(5):1163-1166. doi: 10.1016/j.cell.2016.10.054. Review", + "Mendelson MM, Marioni RE, Joehanes R, Liu C, Hedman ÅK, Aslibekyan S, Demerath EW, Guan W, Zhi D, Yao C, Huan T, Willinger C, Chen B, Courchesne P, Multhaup M, Irvin MR, Cohain A, Schadt EE, Grove ML, Bressler J, North K, Sundström J, Gustafsson S, Shah S, McRae AF, Harris SE, Gibson J, Redmond P, Corley J, Murphy L, Starr JM, Kleinbrink E, Lipovich L, Visscher PM, Wray NR, Krauss RM, Fallin D, Feinberg A, Absher DM, Fornage M, Pankow JS, Lind L, Fox C, Ingelsson E, Arnett DK, Boerwinkle E, Liang L, Levy D, Deary IJ. (2017). Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach. PLoS Med.. 14(1):e1002215. doi: 10.1371/journal.pmed.1002215", + "Bujold D, Morais DA, Gauthier C, Côté C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PÉ, Bourque G. (2016). The International Human Epigenome Consortium Data Portal. Cell Syst. 3(5):496-499.e2. doi: 10.1016/j.cels.2016.10.019", + "Johnson KC, Houseman EA, King JE, Christensen BC. (2017). DNA methylation differences at regulatory elements are associated with the cancer risk factor age in normal breast tissue. bioRxiv doi: 10.1101/101287", + "Li Y, Xu Q, Lv N, Wang L, Zhao H, Wang X, Guo J, Chen C, Li Y, Yu L. (2017). Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia. J Hematol Oncol. 2017 Feb 2;10(1):41. doi: 10.1186/s13045-017-0409-z. Review", + "Ligthart S, Marzi C, Aslibekyan S, Mendelson MM, Conneely KN, Tanaka T, Colicino E, Waite LL, Joehanes R, Guan W, Brody JA, Elks C, Marioni R, Jhun MA, Agha G, Bressler J, Ward-Caviness CK, Chen BH, Huan T, Bakulski K, Salfati EL; WHI-EMPC Investigators., Fiorito G; CHARGE epigenetics of Coronary Heart Disease., Wahl S, Schramm K, Sha J, Hernandez DG, Just AC, Smith JA, Sotoodehnia N, Pilling LC, Pankow JS, Tsao PS, Liu C, Zhao W, Guarrera S, Michopoulos VJ, Smith AK, Peters MJ, Melzer D, Vokonas P, Fornage M, Prokisch H, Bis JC, Chu AY, Herder C, Grallert H, Yao C, Shah S, McRae AF, Lin H, Horvath S, Fallin D, Hofman A, Wareham NJ, Wiggins KL, Feinberg AP, Starr JM, Visscher PM, Murabito JM, Kardia SL, Absher DM, Binder EB, Singleton AB, Bandinelli S, Peters A, Waldenberger M, Matullo G, Schwartz JD, Demerath EW, Uitterlinden AG, van Meurs JB, Franco OH, Chen YI, Levy D, Turner ST, Deary IJ, Ressler KJ, Dupuis J, Ferrucci L, Ong KK, Assimes TL, Boerwinkle E, Koenig W, Arnett DK, Baccarelli AA, Benjamin EJ, Dehghan A. (2016). DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biol. 17(1):255. doi: 10.1186/s13059-016-1119-5", + "Rodger EJ, Chatterjee A. (2017). The epigenomic basis of common diseases. Clin Epigenetics. 9:5. doi: 10.1186/s13148-017-0313-y", "Lewis J, Breeze CE, Charlesworth J, Maclaren OJ, Cooper J. (2016). Where next for the reproducibility agenda in computational biology? BMC Syst. Biol. 10(1):52 doi: 10.1186/s12918-016-0288-x", "Bartlett TE, Chindera K, McDermott J, Breeze CE, Cooke WR, Jones A, Reisel D, Karegodar ST, Arora R, Beck S, Menon U, Dubeau L, Widschwendter M. (2016). Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat. Commun. 7:11620. doi: 10.1038/ncomms11620", "van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S; BIOS Consortium., Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI. (2016). Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat. Commun. 7:11115. doi: 10.1038/ncomms11115");