BokehJS 2.3.0 successfully loaded.

RNA-seq-like Gene Centric Signature Reverse Search (RGCSRS)

Input gene: BRD7

BRD7 is not a landmark gene.

BRD7 is an originally inferred L1000 gene.

BRD7 is a newly inferred (our model) gene.

More information about BRD7 can be found at the Gene and Drug Landing Page Aggregator

Input cell line: All

This Appyter provides visualizations of the top 5% of RNA-seq-like signatures induced by CRISPR knockouts and chemical perturbagens. Signatures are computed from transformed data profiles from the LINCS L1000 data. The transformation was performed using a two-step model:

  1. A cycleGAN model was used to first predict the RNA-seq expression of the 978 L1000 landmark genes
  2. A fully connected neural network was used to extrapolate the predicted RNA-seq expression of the 978 landmark genes to a full set of 23,164 genes

Signatures were computed using the characteristic direction method (Clark et al., 2014), as implemented here.

Each gene was pre-queried across all available RNA-seq-like signatures, and the top signatures where a gene is up or down-regulated are returned for each gene.

CRISPR KO signatures

Volcano Plots

In the following volcano plot, each point represents a single CRISPR knockout signature. The x-position indicates the log2(fold change) of the expression of the chosen gene in the signature, while the y-position indicates the absolute value of the characteristic direction coefficient of the chosen gene.

Note that the fold change and characteristic direction coefficients of the gene are not necessarily in the same direction for each signature; this is because in cases where a gene is both up- and down-regulated between replicate samples, the characteristic direction method prioritizes the more consistent direction of movement, which may not be consistent with the fold change. To read more about the characteristic direction method, please refer to Clark et al., 2014.

Points with same-direction fold change and CD coefficient values are highlighted by coloring them blue (up-regulated) or red (down-regulated). Darker colored points indicate higher differential expression of the gene in the corresponding signature.

Drag the plot to pan around. Use the toolbar to the right of the plot to zoom, reset the plot view, or download the plot.

Tables

The tables below display the characteristic direction (CD) coefficients, fold change values, and log2(fold change) values correponding to the expression of the chosen gene in each CRIPSR KO signature.

The rank of the gene in the signature is determined by its fold change relative to the fold change of the other genes that are regulated in the same direction; if a gene is ranked 1 in a signature where the gene is up-regulated, that means that out of all genes up-regulated in the signature, the input gene had the highest fold change and was the most up-regulated.

While only the top 10 signatures for each direction are displayed, below each table is a link to download the top 50 signatures for each direction.

A link to the Enrichr analysis results of the top 20 unique perturbations from the top signatures that up or down-regulate the input gene can be found below each table as well.

Top CRISPR KO signatures where BRD7 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR012_ES2.311_96H_N24_C1QBP 0.0176 1.3437 0.426221 5987.0 C1QBP ES2.311 96h
XPR022_A375.311_96H_A17_PRAM1 0.0177 1.0557 0.078148 7474.0 PRAM1 A375.311 96h
XPR040_U251MG.311_96H_H02_POLR1C 0.0170 1.0554 0.077812 3944.0 POLR1C U251MG.311 96h
XPR024_YAPC.311_96H_L05_SLC4A11 0.0181 1.0401 0.056705 3847.0 SLC4A11 YAPC.311 96h
XPR020_MCF7.311_96H_C06_MCAM 0.0177 1.0388 0.054959 5511.0 MCAM MCF7.311 96h
XPR030_PC3.311B_96H_B18_MRGPRX1 0.0174 1.0382 0.054094 6366.5 MRGPRX1 PC3.311B 96h
XPR012_PC3.311B_96H_P21_BEST1 0.0170 1.0372 0.052672 4203.0 BEST1 PC3.311B 96h
XPR019_MCF7.311_96H_E18_KLRK1 0.0166 1.0370 0.052424 4128.0 KLRK1 MCF7.311 96h
XPR022_A375.311_96H_P07_RB1 0.0174 1.0370 0.052355 5933.0 RB1 A375.311 96h
XPRJJ002_A375_96H_D11_CBX8 0.0168 1.0348 0.049322 5361.0 CBX8 A375 96h
Top CRISPR KO signatures where BRD7 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR010_MCF7.311_96H_C24_CYP2E1 -0.0172 0.9533 -0.068946 6161.0 CYP2E1 MCF7.311 96h
XPR027_MCF7.311_96H_D24_TFF2 -0.0168 0.9555 -0.065661 6275.0 TFF2 MCF7.311 96h
XPR024_ES2.311_96H_E19_SIGLEC12 -0.0172 0.9557 -0.065389 6404.0 SIGLEC12 ES2.311 96h
XPR024_MCF7.311_96H_O01_SIRPG -0.0171 0.9616 -0.056479 4251.0 SIRPG MCF7.311 96h
XPR025_PC3.311B_96H_P02_TLR2 -0.0169 0.9650 -0.051329 5211.0 TLR2 PC3.311B 96h
XPR022_PC3.311B_96H_G16_PTPRK -0.0174 0.9667 -0.048852 4639.0 PTPRK PC3.311B 96h
XPRJJ002_A375_96H_F08_PIK3CA -0.0176 0.9679 -0.047106 6720.0 PIK3CA A375 96h
XPR022_U251MG.311_96H_G18_PSMA5 -0.0164 0.9691 -0.045325 7969.0 PSMA5 U251MG.311 96h
XPR040_DANG.311_96H_M23_TPR -0.0174 0.9696 -0.044482 8457.0 TPR DANG.311 96h
XPR012_PC3.311B_96H_C03_ASCL2 -0.0184 0.9698 -0.044239 6496.0 ASCL2 PC3.311B 96h

Chemical perturbation signatures

Volcano Plots

In the following volcano plot, each point represents a single chemical perturbation signature. The x-position indicates the log2(fold change) of the expression of the chosen gene in the signature, while the y-position indicates the absolute value of the characteristic direction coefficient of the chosen gene.

Note that the fold change and characteristic direction coefficients of the gene are not necessarily in the same direction for each signature; this is because in cases where a gene is both up- and down-regulated between replicate samples, the characteristic direction method prioritizes the more consistent direction of movement, which may not be consistent with the fold change. To read more about the characteristic direction method, please refer to Clark et al., 2014.

Points with same-direction fold change and CD coefficient values are highlighted by coloring them blue (up-regulated) or red (down-regulated). Darker colored points indicate higher differential expression of the gene in the corresponding signature.

Drag the plot to pan around. Use the toolbar to the right of the plot to zoom, reset the plot view, or download the plot.

Tables

The tables below display the characteristic direction (CD) coefficients, fold change values, and log2(fold change) values correponding to the expression of the chosen gene in each chemical perturbation signature.

The rank of the gene in the signature is determined by its fold change relative to the fold change of the other genes that are regulated in the same direction; if a gene is ranked 1 in a signature where the gene is up-regulated, that means that out of all genes up-regulated in the signature, the input gene had the highest fold change and was the most up-regulated.

While only the top 10 signatures for each direction are displayed, below each table is a link to download the top 50 signatures for each direction.

A link to the Enrichr analysis results of the top 20 unique perturbations from the top signatures that up or down-regulate the input gene can be found below each table as well.

Top chemical perturbation signatures where BRD7 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
REP.A026_MCF7_24H_I19_ARN-509_10uM -0.0194 1.4296 0.515655 16675.0 ARN-509 10uM MCF7 24h
MUC.CP006_MCF7_6H_D15_SA-102676_1.11uM 0.0197 1.1027 0.141026 4219.0 SA-102676 1.11uM MCF7 6h
CPC006_HT115_6H_G17_cyclosporin-a_10uM 0.0192 1.1012 0.139076 2897.0 cyclosporin-a 10uM HT115 6h
CPC003_VCAP_24H_G11_trimethobenzamide_10uM 0.0222 1.0830 0.115072 2611.0 trimethobenzamide 10uM VCAP 24h
MOAR009_22RV1_24H_I24_defactinib_1.11uM 0.0192 1.0651 0.090975 5509.0 defactinib 1.11uM 22RV1 24h
CPC005_A549_24H_C07_chlorphensin_10uM 0.0210 1.0607 0.085076 6120.0 chlorphensin 10uM A549 24h
REP.B015_MCF7_24H_G06_tiapride_0.01uM 0.0196 1.0574 0.080581 4248.0 tiapride 0.01uM MCF7 24h
ABY001_HT29_XH_I04_lapatinib_10uM 0.0199 1.0560 0.078607 6206.0 lapatinib 10uM HT29 xh
CPC006_MCF7_24H_C13_YK-4279_10uM 0.0213 1.0528 0.074178 7821.0 YK-4279 10uM MCF7 24h
CPC018_ASC_24H_N17_mebendazole_10uM 0.0205 1.0509 0.071661 4562.0 mebendazole 10uM ASC 24h
Top chemical perturbation signatures where BRD7 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
PAC036_U2OS_6H_H19_wortmannin_20uM -0.0186 0.8791 -0.185936 5324.0 wortmannin 20uM U2OS 6h
CPC011_MCF7_6H_M20_zileuton_10uM -0.0187 0.8961 -0.158306 4042.0 zileuton 10uM MCF7 6h
LJP005_A549_24H_I10_CP-466722_0.37uM -0.0199 0.9264 -0.110243 5326.0 CP-466722 0.37uM A549 24h
REP.A023_MCF7_24H_D11_amsacrine_0.125uM -0.0198 0.9281 -0.107602 6126.0 amsacrine 0.125uM MCF7 24h
ISO001_MCF10A.EGFR.HD_24H_P23_vemurafenib_0.12uM -0.0204 0.9347 -0.097469 6750.0 vemurafenib 0.12uM MCF10A.EGFR.HD 24h
REP.B018_A375_24H_F04_JTE-907_0.08uM -0.0210 0.9367 -0.094345 4501.0 JTE-907 0.08uM A375 24h
REP.B004_MCF7_24H_K15_TIC-10_0.25uM -0.0207 0.9449 -0.081799 4474.0 TIC-10 0.25uM MCF7 24h
CPD002_PC3_6H_B10_citiolone_10uM -0.0189 0.9462 -0.079718 3549.0 citiolone 10uM PC3 6h
REP.A006_A375_24H_O22_efatutazone_0.37uM -0.0213 0.9545 -0.067210 5209.0 efatutazone 0.37uM A375 24h
EMU001_KMS34_24H_N14_parthenolide_2.5uM -0.0187 0.9549 -0.066533 4655.0 parthenolide 2.5uM KMS34 24h