MSigDB v6.2 Release Notes - Revision history https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v6.2_Release_Notes&action=history Revision history for this page on the wiki en MediaWiki 1.34.4 Fri, 29 Mar 2024 14:19:52 GMT Helga at 15:31, 12 July 2018 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v6.2_Release_Notes&diff=4229&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v6.2_Release_Notes&diff=4229&oldid=prev <p></p> <p><b>New page</b></p><div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> &lt;p&gt;This page describes the changes made to the gene set collections for Release 6.2 of the Molecular Signatures Database (MSigDB). This is a minor release that includes updates to gene set annotations, corrections to miscellaneous errors, and a handful of new gene sets.&lt;/p&gt;<br /> &lt;h2&gt;New Gene Sets&lt;/h2&gt;<br /> We added the following 24 new gene sets to the C2:CGP collection.<br /> <br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 &lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; AANDERSEN_CHOLANGIOCARCINOMA_CLASS1&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; AOISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; AVILLANUEVA_LIVER_CANCER_KRT19_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; AMINGUEZ_LIVER_CANCER_VASCULAR_INVASION_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; ANDERSEN_LIVER_CANCER_KRT19_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KIM_LIVER_CANCER_POOR_SURVIVAL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_ADENOMYOEPITHELIAL_BREAST_TUMOR&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_EMT_BREAST_TUMOR_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_SQUAMOUS_BREAST_TUMOR&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_PAPILLARY_BREAST_TUMOR&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_MICROACINAR_BREAST_TUMOR_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; HOLLERN_SOLID_NODULAR_BREAST_TUMOR_UP &amp; DN &lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; FLORIO_HUMAN_NEOCORTEX&lt;br&gt;<br /> <br /> &lt;h2&gt;Annotation Updates&lt;/h2&gt;<br /> • We normalized the '''Contributor''' information to have more consistent values. This affects 12,858 sets across MSigDB.<br /> <br /> • We updated the '''Exact Source''' field to reference the appropriate identifiers from the contributing source in the KEGG, Reactome, Signaling Transduction KE, and SuperArray sets in the C2:CP collection, the WARTERS_IR_RESPONSE_5GY gene set in the C2:CGP collection, and all sets in the C4:CM and C5 collections<br /> <br /> • We filled in the missing '''Full Description''' for 2 sets in the C2:CGP collection, 196 sets in the C2:CP collection, and 28 sets in the C6 collection. <br /> <br /> • We filled in missing '''Source Publication''' information for 196 sets in the C2:CP collection.<br /> <br /> • We removed the obsolete '''External Links''' for all Signaling Transduction KE, SigmaAldrich, SuperArray, and Pathway Interaction Database (PID) sets in the C2:CP collection, as the referenced pages have been removed from the third-party websites.<br /> <br /> &lt;h2&gt;Name Changes&lt;/h2&gt;<br /> • We corrected inadvertent reversals of UP and DN naming of the following sets:&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp; PRC1_BMI_UP.V1_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp; PRC2_EZH2_UP.V1_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp; PRC2_EZH2_UP.V1_UP &amp; DN&lt;br&gt;<br /> <br /> • We corrected the MOHANKUMAR_TLX1_TARGETS_UP &amp; DN sets to refer to HOXA1 instead of TLX1. These thus become MOHANKUMAR_HOXA1_TARGETS_UP &amp; DN. We also updated the corresponding founder gene set references in HALLMARK_MTORC1_SIGNALING.<br /> <br /> • We renamed the following sets to remove problematic dash characters: &lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GNF2_HLA_C&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE15930_STIM_VS_STIM_AND_IL12_24H_CD8_T_CELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE15930_STIM_VS_STIM_AND_IL12_48H_CD8_T_CELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE15930_STIM_VS_STIM_AND_IL12_72H_CD8_T_CELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE6090_UNSTIM_VS_DC_SIGN_STIM_DC_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE12505_WT_VS_E2_2_HET_PDC_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE24726_WT_VS_E2_2_KO_PDC_DAY6_POST_DELETION_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE24726_WT_VS_E2_2_KO_PDC_DAY4_POST_DELETION_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; GSE24726_WT_VS_E2_2_KO_PDC_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; MATZUK_POSTIMPLANTATION_AND_POSTPARTUM&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; STEGMEIER_PREMITOTIC_CELL_CYCLE_REGULATORS&lt;br&gt;<br /> <br /> &lt;h2&gt;Other Corrections&lt;/h2&gt;<br /> We corrected the following errors:<br /> <br /> • Typing errors in the '''Brief Description''' of ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN (C2:CGP collection) and MTOR_UP.N4.V1_UP &amp; DN (C6 collection).<br /> <br /> • Issues in the '''Member''' mapping for QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR and MACAEVA_PBMC_RESPONSE_TO_IR (C2:CGP collection).<br /> <br /> • Incorrect '''Source Platform''' in the RAPA_EARLY_UP.V1_UP &amp; DN sets (C6 collection).<br /> <br /> • Transpositions among sets and some typing errors in the brief description for the 12 KAECH sets (C7 collection). &lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_NAIVE_VS_DAY8_EFF_CD8_TCELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_NAIVE_VS_DAY15_EFF_CD8_TCELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_NAIVE_VS_MEMORY_CD8_TCELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_DAY8_EFF_VS_DAY15_EFF_CD8_TCELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_DAY8_EFF_VS_MEMORY_CD8_TCELL_UP &amp; DN&lt;br&gt;<br /> &amp;nbsp;&amp;nbsp;&amp;nbsp; KAECH_DAY15_EFF_VS_MEMORY_CD8_TCELL_UP &amp; DN&lt;br&gt;</div> Thu, 12 Jul 2018 15:31:05 GMT Helga https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v6.2_Release_Notes