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

Input gene: MED23

MED23 is not a landmark gene.

MED23 is an originally inferred L1000 gene.

MED23 is a newly inferred (our model) gene.

More information about MED23 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 MED23 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR038_A549.311_96H_H06_EHF 0.0155 1.0560 0.078556 5778.0 EHF A549.311 96h
XPR019_U251MG.311_96H_L24_LRRC8C 0.0160 1.0505 0.071103 4351.0 LRRC8C U251MG.311 96h
XPR026_HT29.311_96H_A05_TMEM120A 0.0170 1.0493 0.069389 4565.0 TMEM120A HT29.311 96h
XPR032_A375.311_96H_G21_LIPT1 0.0154 1.0470 0.066302 4944.0 LIPT1 A375.311 96h
XPR016_ES2.311_96H_K23_CASP3 0.0170 1.0447 0.063049 6039.0 CASP3 ES2.311 96h
XPR030_A549.311_96H_M21_ALDH7A1 0.0163 1.0355 0.050322 4970.0 ALDH7A1 A549.311 96h
XPR040_HS944T.311_96H_B09_ARPC3 0.0156 1.0353 0.050024 8032.0 ARPC3 HS944T.311 96h
XPR032_A375.311_96H_G02_GCSH 0.0159 1.0352 0.049943 5707.0 GCSH A375.311 96h
XPR018_YAPC.311_96H_F24_KAT6A 0.0157 1.0346 0.049121 4883.0 KAT6A YAPC.311 96h
XPR008_YAPC.311_96H_K23_GRM2 0.0153 1.0344 0.048780 4308.0 GRM2 YAPC.311 96h
Top CRISPR KO signatures where MED23 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR021_U251MG.311_96H_H03_NOBOX -0.0171 0.9009 -0.150519 5261.0 NOBOX U251MG.311 96h
XPR019_MCF7.311_96H_M09_KDM4E -0.0163 0.9039 -0.145704 4465.0 KDM4E MCF7.311 96h
XPR041_HCC1806.311_96H_I21_MAP4K1 -0.0153 0.9257 -0.111366 6860.0 MAP4K1 HCC1806.311 96h
XPR036_PC3.311B_96H_O12_GUCY2C -0.0166 0.9368 -0.094154 5224.0 GUCY2C PC3.311B 96h
XPR038_SNU761.311_96H_F11_NDFIP1 -0.0157 0.9455 -0.080907 5711.0 NDFIP1 SNU761.311 96h
XPR015_MCF7.311_96H_H17_CYP4F3 -0.0163 0.9516 -0.071498 2943.0 CYP4F3 MCF7.311 96h
XPR032_U251MG.311_96H_P09_TNFRSF10B -0.0158 0.9631 -0.054171 4575.0 TNFRSF10B U251MG.311 96h
XPR010_AGS.311_96H_C09_SV2A -0.0157 0.9637 -0.053384 5782.0 SV2A AGS.311 96h
XPR018_A375.311_96H_F19_IRF2 -0.0158 0.9673 -0.047895 4812.0 IRF2 A375.311 96h
XPR023_HT29.311_96H_F07_SCUBE1 -0.0162 0.9686 -0.046065 4305.0 SCUBE1 HT29.311 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 MED23 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
ERG011_VCAP_24H_J07_PP-242_10uM 0.0174 1.2252 0.293051 4214.0 PP-242 10uM VCAP 24h
LJP006_LNCAP_24H_F19_QL-X-138_10uM 0.0174 1.2008 0.264013 4928.0 QL-X-138 10uM LNCAP 24h
PBIOA020_A549_24H_H03_LY-2183240_1.11uM 0.0169 1.1271 0.172565 1958.0 LY-2183240 1.11uM A549 24h
MUC.CP006_MCF7_6H_G06_GW-843682X_3.33uM 0.0179 1.1150 0.157087 5449.0 GW-843682X 3.33uM MCF7 6h
CPC002_VCAP_24H_J04_GR-55562_10uM 0.0176 1.1108 0.151576 5947.0 GR-55562 10uM VCAP 24h
LUNG001_NL20_24H_I09_terreic-acid_10uM 0.0198 1.1020 0.140172 5607.0 terreic-acid 10uM NL20 24h
LJP008_MCF7_24H_B07_GSK-461364_10uM 0.0170 1.1010 0.138860 3520.0 GSK-461364 10uM MCF7 24h
ISO001_MCF10A.EGFR.HL_24H_G05_afatinib_0.12uM 0.0176 1.1010 0.138854 4721.0 afatinib 0.12uM MCF10A.EGFR.HL 24h
REP.A024_MCF7_24H_N02_crizotinib_3.33uM 0.0185 1.0961 0.132341 3158.0 crizotinib 3.33uM MCF7 24h
REP.B019_MCF7_24H_D20_CC-401_0.74uM 0.0189 1.0830 0.115009 3841.0 CC-401 0.74uM MCF7 24h
Top chemical perturbation signatures where MED23 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
DOS011_VCAP_24H_C16_withaferin-a_10uM -0.0190 0.6683 -0.581522 1896.0 withaferin-a 10uM VCAP 24h
CRCGN015_HEPG2_48H_C19_mitoxantrone_10uM -0.0168 0.7630 -0.390206 3663.0 mitoxantrone 10uM HEPG2 48h
PBIOA018_MCF7_24H_O08_doxorubicin_3.33uM -0.0193 0.8248 -0.277929 4374.0 doxorubicin 3.33uM MCF7 24h
REP.A004_PC3_24H_I14_tafamidis-meglumine_3.33uM -0.0178 0.8353 -0.259678 4742.0 tafamidis-meglumine 3.33uM PC3 24h
MUC.CP004_MCF7_6H_K22_SA-425929_3.33uM -0.0190 0.8507 -0.233348 2637.0 SA-425929 3.33uM MCF7 6h
MOAR008_SKES1_24H_L18_PSB-11_1.11uM -0.0169 0.8935 -0.162435 2965.0 PSB-11 1.11uM SKES1 24h
ISO001_MCF10A.WTLP_24H_H08_sirolimus_3.33uM -0.0187 0.9018 -0.149140 6081.0 sirolimus 3.33uM MCF10A.WTLP 24h
CPD001_MCF7_24H_I09_isoxicam_10uM -0.0178 0.9027 -0.147683 4894.0 isoxicam 10uM MCF7 24h
PBIOA016_HA1E_24H_M04_SB-743921_0.37uM -0.0171 0.9053 -0.143554 4631.0 SB-743921 0.37uM HA1E 24h
CPC017_MCF7_6H_L24_ipratropium_10uM -0.0180 0.9368 -0.094206 3785.0 ipratropium 10uM MCF7 6h