MSigDB v6.2 (Jul 2018)
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
This table shows the corrected names of gene sets MSigDB v6.2 and the former name in v6.1.
| **v6.2 corrected name** | **v6.1 former name** |
| MOHANKUMAR_HOXA1_TARGETS_UP | MOHANKUMAR_TLX1_TARGETS_UP |
| MOHANKUMAR_HOXA1_TARGETS_DN | MOHANKUMAR_TLX1_TARGETS_DN |
| PRC1_BMI_UP.V1_UP | PRC1_BMI_UP.V1_DN |
| PRC1_BMI_UP.V1_DN | PRC1_BMI_UP.V1_UP |
| PRC2_EZH2_UP.V1_UP | PRC2_EZH2_UP.V1_DN |
| PRC2_EZH2_UP.V1_DN | PRC2_EZH2_UP.V1_UP |
| PRC2_EZH2_UP.V1_UP | PRC2_EZH2_UP.V1_DN |
| PRC2_EZH2_UP.V1_DN | PRC2_EZH2_UP.V1_UP |
| GNF2_HLA_C | GNF2_HLA-C |
| STEGMEIER_PREMITOTIC_CELL_CYCLE_REGULATORS | STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS |
| MATZUK_POSTIMPLANTATION_AND_POSTPARTUM | MATZUK_POST-IMPLANTATION_AND_POST-PARTUM |
| GSE15930_STIM_VS_STIM_AND_IL12_24H_CD8_T_CELL_UP | GSE15930_STIM_VS_STIM_AND_IL-12_24H_CD8_T_CELL_UP |
| GSE15930_STIM_VS_STIM_AND_IL12_24H_CD8_T_CELL_DN | GSE15930_STIM_VS_STIM_AND_IL-12_24H_CD8_T_CELL_DN |
| GSE15930_STIM_VS_STIM_AND_IL12_48H_CD8_T_CELL_UP | GSE15930_STIM_VS_STIM_AND_IL-12_48H_CD8_T_CELL_UP |
| GSE15930_STIM_VS_STIM_AND_IL12_48H_CD8_T_CELL_DN | GSE15930_STIM_VS_STIM_AND_IL-12_48H_CD8_T_CELL_DN |
| GSE15930_STIM_VS_STIM_AND_IL12_72H_CD8_T_CELL_UP | GSE15930_STIM_VS_STIM_AND_IL-12_72H_CD8_T_CELL_UP |
| GSE15930_STIM_VS_STIM_AND_IL12_72H_CD8_T_CELL_DN | GSE15930_STIM_VS_STIM_AND_IL-12_72H_CD8_T_CELL_DN |
| GSE6090_UNSTIM_VS_DC_SIGN_STIM_DC_UP | GSE6090_UNSTIM_VS_DC-SIGN_STIM_DC_UP |
| GSE6090_UNSTIM_VS_DC_SIGN_STIM_DC_DN | GSE6090_UNSTIM_VS_DC-SIGN_STIM_DC_DN |
| GSE12505_WT_VS_E2_2_HET_PDC_UP | GSE12505_WT_VS_E2-2_HET_PDC_UP |
| GSE12505_WT_VS_E2_2_HET_PDC_DN | GSE12505_WT_VS_E2-2_HET_PDC_DN |
| GSE24726_WT_VS_E2_2_KO_PDC_DAY6_POST_DELETION_DN | GSE24726_WT_VS_E2-2_KO_PDC_DAY6_POST_DELETION_DN |
| GSE24726_WT_VS_E2_22_KO_PDC_DAY4_POST_DELETION_DN | GSE24726_WT_VS_E2-2_KO_PDC_DAY4_POST_DELETION_DN |
| GSE24726_WT_VS_E2_2_KO_PDC_UP | GSE24726_WT_VS_E2-2_KO_PDC_UP |
| GSE24726_WT_VS_E2_2_KO_PDC_DN | GSE24726_WT_VS_E2-2_KO_PDC_DN |
| GSE24726_WT_VS_E2_2_KO_PDC_DAY6_POST_DELETION_UP | GSE24726_WT_VS_E2-2_KO_PDC_DAY6_POST_DELETION_UP |
| GSE24726_WT_VS_E2_2_KO_PDC_DAY4_POST_DELETION_UP | GSE24726_WT_VS_E2-2_KO_PDC_DAY4_POST_DELETION_UP |