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

Input gene: FZD9

FZD9 is not a landmark gene.

FZD9 is an originally inferred L1000 gene.

FZD9 is a newly inferred (our model) gene.

More information about FZD9 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 FZD9 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR027_A375.311_96H_A23_VPS18 0.0229 1.8871 0.916180 487.0 VPS18 A375.311 96h
XPR037_PC3.311B_96H_D19_GCSAML 0.0197 1.7776 0.829956 209.0 GCSAML PC3.311B 96h
XPR031_ES2.311_96H_O13_OSBPL6 0.0191 1.7610 0.816365 251.0 OSBPL6 ES2.311 96h
XPR043_KELLY.311_96H_K10_PIP4K2B 0.0191 1.6959 0.762086 170.0 PIP4K2B KELLY.311 96h
XPR032_PC3.311B_96H_L15_IL5 0.0201 1.6260 0.701308 337.0 IL5 PC3.311B 96h
XPR036_PC3.311B_96H_G14_PFKFB1 0.0194 1.5541 0.636100 141.0 PFKFB1 PC3.311B 96h
XPR043_ES2.311_96H_E08_MIF 0.0192 1.5381 0.621181 222.0 MIF ES2.311 96h
XPR036_ES2.311_96H_K08_RIOK1 0.0201 1.5265 0.610238 204.0 RIOK1 ES2.311 96h
XPR033_PC3.311B_96H_J06_ERO1B 0.0201 1.5203 0.604389 296.0 ERO1B PC3.311B 96h
XPR036_PC3.311B_96H_E16_CERKL 0.0197 1.5158 0.600105 178.0 CERKL PC3.311B 96h
Top CRISPR KO signatures where FZD9 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature KO Gene Cell Line Timepoint
Signature
XPR034_PC3.311B_96H_E23_RBP1 -0.0201 0.2225 -2.168265 61.0 RBP1 PC3.311B 96h
XPR032_PC3.311B_96H_G17_SOD1 -0.0188 0.3389 -1.560924 128.0 SOD1 PC3.311B 96h
XPR017_ES2.311_96H_G02_HAMP -0.0188 0.3407 -1.553416 159.0 HAMP ES2.311 96h
XPR030_PC3.311B_96H_C21_GPX3 -0.0187 0.3497 -1.515713 274.0 GPX3 PC3.311B 96h
XPR009_U251MG.311_96H_L22_ARFGEF2 -0.0187 0.5236 -0.933485 487.0 ARFGEF2 U251MG.311 96h
XPR030_PC3.311B_96H_A09_GSR -0.0203 0.5445 -0.877044 247.0 GSR PC3.311B 96h
XPR029_A375.311_96H_O23_PLOD3 -0.0185 0.5619 -0.831544 479.0 PLOD3 A375.311 96h
XPR009_ES2.311_96H_E10_PDE2A -0.0229 0.6003 -0.736282 458.0 PDE2A ES2.311 96h
XPR008_U251MG.311_96H_D17_KCNK9 -0.0204 0.6326 -0.660661 535.0 KCNK9 U251MG.311 96h
XPR015_ES2.311_96H_C05_CRB1 -0.0211 0.6351 -0.654872 487.0 CRB1 ES2.311 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 FZD9 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
REP.A025_A375_24H_G15_bortezomib_20uM 0.0219 1.9534 0.965984 1536.0 bortezomib 20uM A375 24h
MOAR011_MELHO_24H_N20_CHIR-124_3.33uM 0.0223 1.8156 0.860415 605.0 CHIR-124 3.33uM MELHO 24h
LJP006_HS578T_24H_K21_JNK-9L_1.11uM 0.0235 1.6832 0.751235 601.0 JNK-9L 1.11uM HS578T 24h
MOAR010_BC3C_24H_C17_thalidomide_3.33uM 0.0218 1.5217 0.605722 481.0 thalidomide 3.33uM BC3C 24h
MOAR008_HEC251_24H_E02_velnacrine_3.33uM 0.0232 1.5133 0.597717 547.0 velnacrine 3.33uM HEC251 24h
MOAR009_HEC1A_24H_O16_LY-2979165_10uM 0.0233 1.4665 0.552333 524.0 LY-2979165 10uM HEC1A 24h
REP.A016_MDAMB231_24H_A24_palbociclib_0.04uM 0.0245 1.4403 0.526410 429.0 palbociclib 0.04uM MDAMB231 24h
MOAR012_BC3C_24H_I02_zaltoprofen_3.33uM 0.0209 1.4315 0.517477 602.0 zaltoprofen 3.33uM BC3C 24h
REP.A016_A375_24H_L12_DMP-777_0.04uM 0.0208 1.3044 0.383348 496.0 DMP-777 0.04uM A375 24h
MOAR009_HEC1A_24H_P16_ligustilide_10uM 0.0211 1.2833 0.359896 757.0 ligustilide 10uM HEC1A 24h
Top chemical perturbation signatures where FZD9 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
REP.B014_MDAMB231_24H_C09_Y-39983_0.25uM -0.0205 0.2713 -1.882187 196.0 Y-39983 0.25uM MDAMB231 24h
REP.A016_MDAMB231_24H_M21_Y-27632_1.11uM -0.0214 0.4828 -1.050519 533.0 Y-27632 1.11uM MDAMB231 24h
MOAR009_HEC1A_24H_O15_MSX-122_1.11uM -0.0242 0.5404 -0.887829 427.0 MSX-122 1.11uM HEC1A 24h
MOAR008_OVTOKO_24H_D03_DPO-1_1.11uM -0.0215 0.5713 -0.807604 455.0 DPO-1 1.11uM OVTOKO 24h
REP.A006_PC3_24H_P23_AT-9283_0.125uM -0.0213 0.5893 -0.762867 335.0 AT-9283 0.125uM PC3 24h
CRCGN009_HEPG2_24H_P03_sorbic-acid_10uM -0.0219 0.5977 -0.742505 949.0 sorbic-acid 10uM HEPG2 24h
REP.A020_PC3_24H_E23_edoxudine_0.125uM -0.0224 0.5995 -0.738239 593.0 edoxudine 0.125uM PC3 24h
REP.A007_HA1E_24H_D13_pidotimod_10uM -0.0224 0.6100 -0.713024 589.0 pidotimod 10uM HA1E 24h
REP.A021_MDAMB231_24H_G20_mirodenafil_3.33uM -0.0239 0.6327 -0.660298 754.0 mirodenafil 3.33uM MDAMB231 24h
REP.A016_MDAMB231_24H_G12_vinpocetine_0.04uM -0.0237 0.6356 -0.653743 668.0 vinpocetine 0.04uM MDAMB231 24h