MSigDB v6.2 Release Notes

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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.

New Gene Sets

We added the following 24 new gene sets to the C2:CGP collection.

    ANDERSEN_CHOLANGIOCARCINOMA_CLASS2
    AANDERSEN_CHOLANGIOCARCINOMA_CLASS1
    AOISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP & DN
    AVILLANUEVA_LIVER_CANCER_KRT19_UP & DN
    AMINGUEZ_LIVER_CANCER_VASCULAR_INVASION_UP & DN
    ANDERSEN_LIVER_CANCER_KRT19_UP & DN
    KIM_LIVER_CANCER_POOR_SURVIVAL_UP & DN
    HOLLERN_ADENOMYOEPITHELIAL_BREAST_TUMOR
    HOLLERN_EMT_BREAST_TUMOR_UP & DN
    HOLLERN_SQUAMOUS_BREAST_TUMOR
    HOLLERN_PAPILLARY_BREAST_TUMOR
    HOLLERN_MICROACINAR_BREAST_TUMOR_UP & DN
    HOLLERN_SOLID_NODULAR_BREAST_TUMOR_UP & DN
    FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_UP & DN
    FLORIO_HUMAN_NEOCORTEX

Annotation Updates

• We normalized the Contributor information to have more consistent values. This affects 12,858 sets across MSigDB.

• 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

• 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.

• We filled in missing Source Publication information for 196 sets in the C2:CP collection.

• 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.

Name Changes

• We corrected inadvertent reversals of UP and DN naming of the following sets:
   PRC1_BMI_UP.V1_UP & DN
   PRC2_EZH2_UP.V1_UP & DN
   PRC2_EZH2_UP.V1_UP & DN

• We corrected the MOHANKUMAR_TLX1_TARGETS_UP & DN sets to refer to HOXA1 instead of TLX1. These thus become MOHANKUMAR_HOXA1_TARGETS_UP & DN. We also updated the corresponding founder gene set references in HALLMARK_MTORC1_SIGNALING.

• We renamed the following sets to remove problematic dash characters:
    GNF2_HLA_C
    GSE15930_STIM_VS_STIM_AND_IL12_24H_CD8_T_CELL_UP & DN
    GSE15930_STIM_VS_STIM_AND_IL12_48H_CD8_T_CELL_UP & DN
    GSE15930_STIM_VS_STIM_AND_IL12_72H_CD8_T_CELL_UP & DN
    GSE6090_UNSTIM_VS_DC_SIGN_STIM_DC_UP & DN
    GSE12505_WT_VS_E2_2_HET_PDC_UP & DN
    GSE24726_WT_VS_E2_2_KO_PDC_DAY6_POST_DELETION_UP & DN
    GSE24726_WT_VS_E2_2_KO_PDC_DAY4_POST_DELETION_UP & DN
    GSE24726_WT_VS_E2_2_KO_PDC_UP & DN
    MATZUK_POSTIMPLANTATION_AND_POSTPARTUM
    STEGMEIER_PREMITOTIC_CELL_CYCLE_REGULATORS

Other Corrections

We corrected the following errors:

• Typing errors in the Brief Description of ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN (C2:CGP collection) and MTOR_UP.N4.V1_UP & DN (C6 collection).

• Issues in the Member mapping for QUINTENS_EMBRYONIC_BRAIN_RESPONSE_TO_IR and MACAEVA_PBMC_RESPONSE_TO_IR (C2:CGP collection).

• Incorrect Source Platform in the RAPA_EARLY_UP.V1_UP & DN sets (C6 collection).

• Transpositions among sets and some typing errors in the brief description for the 12 KAECH sets (C7 collection).
    KAECH_NAIVE_VS_DAY8_EFF_CD8_TCELL_UP & DN
    KAECH_NAIVE_VS_DAY15_EFF_CD8_TCELL_UP & DN
    KAECH_NAIVE_VS_MEMORY_CD8_TCELL_UP & DN
    KAECH_DAY8_EFF_VS_DAY15_EFF_CD8_TCELL_UP & DN
    KAECH_DAY8_EFF_VS_MEMORY_CD8_TCELL_UP & DN
    KAECH_DAY15_EFF_VS_MEMORY_CD8_TCELL_UP & DN