# Filepaths and Hard-coded Defaults
proj_root = "/users/kcochran/projects/procap_models/"
sequence_path = proj_root + "genomes/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
chrom_sizes = proj_root + "genomes/hg38.chrom.sizes.withrRNA"
in_window = 2114
out_window = 1000
# stuff to get from config file
with open("2022-07-04_06-07-54_run1_modisco_config.txt") as config_f:
config_dict = {line.split()[0] : line.strip().split()[1] for line in config_f}
modisco_out_path = config_dict["modisco_out_path"]
scoring_type = config_dict["scoring_type"]
score_center_size = int(config_dict["score_center_size"])
profile_display_center_size = int(config_dict["profile_display_center_size"])
# digest what's in config file
assay_type, model_type, cell, accession, modisco_dir_base = modisco_out_path.split("/")[-5:]
ts_part1, ts_part2, run_str, _ = modisco_dir_base.split("_")
timestamp = ts_part1 + "_" + ts_part2
run = int(run_str.replace("run", ""))
print(modisco_out_path)
print("cell_type:", cell, accession)
print("timestamp:", timestamp)
print("run:", run)
print("scoring_type:", scoring_type)
print("score_center_size:", score_center_size)
print("profile_display_center_size:", profile_display_center_size)
/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/CALU3/ENCSR935RNW/2022-07-04_06-07-54_run1_modisco cell_type: CALU3 ENCSR935RNW timestamp: 2022-07-04_06-07-54 run: 1 scoring_type: counts score_center_size: 1000 profile_display_center_size: 400
data_dir = proj_root + "/data/procap/processed/" + cell + "/" + accession + "/"
plus_bw_path = data_dir + "final.5prime.pos.bigWig"
minus_bw_path = data_dir + "final.5prime.neg.bigWig"
val_peak_path = data_dir + "peaks_uni_and_bi_train_and_val.bed.gz"
val_save_dir = proj_root + "model_out/" + assay_type + "/" + model_type + "/" + cell + "/" + accession + "/"
val_save_path = val_save_dir + timestamp + "_run" + str(run) + "_train_and_val"
attr_save_path = val_save_dir.replace("model_out", "deepshap_out") + timestamp + "_run" + str(run) + "_deepshap"
if not modisco_out_path.endswith("/"):
modisco_out_path = modisco_out_path + "/"
# task-specific filepaths
import os
assert scoring_type in ["profile", "counts"], scoring_type
if scoring_type == "profile":
scores_path = attr_save_path + "_prof.npy"
onehot_scores_path = attr_save_path + "_prof_onehot.npy"
modisco_obj_path = modisco_out_path + "results_allChroms_prof_slice500.hdf5"
seqlet_path = modisco_out_path + "seqlets_prof.txt"
else:
scores_path = attr_save_path + "_count.npy"
onehot_scores_path = attr_save_path + "_count_onehot.npy"
modisco_obj_path = modisco_out_path + "results_allChroms_count_slice500.hdf5"
seqlet_path = modisco_out_path + "seqlets_count.txt"
assert(os.path.exists(scores_path)), scores_path
assert(os.path.exists(onehot_scores_path)), onehot_scores_path
# Imports, Plotting Defaults
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
plot_params = {
"figure.titlesize": 22,
"axes.titlesize": 22,
"axes.labelsize": 20,
"legend.fontsize": 18,
"xtick.labelsize": 16,
"ytick.labelsize": 16,
"font.weight": "bold"
}
plt.rcParams.update(plot_params)
from IPython.display import display
import tqdm
tqdm.tqdm_notebook()
import numpy as np
from view_modisco_results_utils import *
/users/kcochran/miniconda3/envs/procap/lib/python3.7/site-packages/ipykernel_launcher.py:19: TqdmDeprecationWarning: This function will be removed in tqdm==5.0.0 Please use `tqdm.notebook.tqdm` instead of `tqdm.tqdm_notebook`
# Load in True Profiles and Sequences
import sys
sys.path.append('../1_train_models')
from data_loading import extract_peaks
one_hot_seqs, true_profs = extract_peaks(sequence_path,
plus_bw_path, minus_bw_path, val_peak_path, in_window, out_window,
max_jitter=0, verbose=True)
one_hot_seqs = one_hot_seqs.swapaxes(1,2)
one_hot_seqs = one_hot_seqs[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]
Reading FASTA: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 24/24 [00:15<00:00, 1.50it/s] Loading Peaks: 42440it [01:27, 484.73it/s]
# Load in Coordinates of Examples
coords = load_coords(val_peak_path, in_window)
# Import SHAP scores, predicted profiles
hyp_scores = np.load(scores_path).swapaxes(1,2)
hyp_scores = hyp_scores[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]
pred_profs = np.exp(np.load(val_save_path + ".profs.npy"))
# Load modisco results object
tfm_obj = import_tfmodisco_results(modisco_obj_path, hyp_scores, one_hot_seqs)
motif_pfms, motif_hcwms, motif_cwms, \
motif_pfms_short, num_seqlets, \
motif_seqlets, num_metaclusters = plot_all_metaclusters(tfm_obj, one_hot_seqs, hyp_scores,
true_profs, pred_profs, coords,
in_window, out_window,
score_center_size,
profile_display_center_size)
16466 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
12273 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
7315 seqlets
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6561 seqlets
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5651 seqlets
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4446 seqlets
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2981 seqlets
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1194 seqlets
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1095 seqlets
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1018 seqlets
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1008 seqlets
Sequence (PFM) | |
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830 seqlets
Sequence (PFM) | |
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709 seqlets
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552 seqlets
Sequence (PFM) | |
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384 seqlets
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338 seqlets
Sequence (PFM) | |
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332 seqlets
Sequence (PFM) | |
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Actual contributions (CWM) |
314 seqlets
Sequence (PFM) | |
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168 seqlets
Sequence (PFM) | |
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72 seqlets
Sequence (PFM) | |
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22 seqlets
Sequence (PFM) | |
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104 seqlets
Sequence (PFM) | |
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102 seqlets
Sequence (PFM) | |
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87 seqlets
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76 seqlets
Sequence (PFM) | |
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57 seqlets
Sequence (PFM) | |
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55 seqlets
Sequence (PFM) | |
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Actual contributions (CWM) |
50 seqlets
Sequence (PFM) | |
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Actual contributions (CWM) |
48 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
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46 seqlets
Sequence (PFM) | |
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46 seqlets
Sequence (PFM) | |
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36 seqlets
Sequence (PFM) | |
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33 seqlets
Sequence (PFM) | |
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23 seqlets
Sequence (PFM) | |
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Actual contributions (CWM) |
run_and_plot_tomtom(modisco_out_path, motif_pfms, motif_hcwms, motif_pfms_short, num_metaclusters)
The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/CALU3/ENCSR935RNW/2022-07-04_06-07-54_run1_modisco/tomtom' already exists. Its contents will be overwritten. Processing query 1 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.9855 Processing query 2 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.971112 Processing query 3 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 4 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.957097 Processing query 5 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.9855 Processing query 6 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.99552 Processing query 7 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.978413 Processing query 8 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 9 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 10 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.97137 Processing query 11 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.969304 Processing query 12 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.964105 Processing query 13 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.959048 Processing query 14 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.989354 Processing query 15 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.951546 Processing query 16 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 17 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998346 Processing query 18 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.980105 Processing query 19 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.990608 Processing query 20 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.963325 Processing query 21 out of 21 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998346 Can't locate HtmlMonolithWr.pm: /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48. Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.
Motif ID | q-val | PWM |
---|---|---|
MA0026.1-Eip74EF | 2.88216e-05 | |
MA0916.1-Ets21C | 4.67609e-05 | |
MA1483.2-ELF2 | 4.67609e-05 | |
MA0750.2-ZBTB7A | 4.67609e-05 | |
MA0764.3-ETV4 | 6.30128e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1513.1-KLF15 | 4.38475e-05 | |
MA0516.3-SP2 | 0.000162585 | |
MA0685.2-SP4 | 0.000162585 | |
MA0742.2-KLF12 | 0.000162585 | |
MA1511.2-KLF10 | 0.000183661 |
Motif ID | q-val | PWM |
---|---|---|
MA0314.2-HAP3 | 3.56007e-05 | |
MA0060.3-NFYA | 3.56007e-05 | |
MA1644.1-NFYC | 3.56007e-05 | |
MA0502.2-NFYB | 0.00844247 | |
MA0316.1-HAP5 | 0.0137046 |
Motif ID | q-val | PWM |
---|---|---|
MA1475.1-CREB3L4 | 0.00397176 | |
MA1140.2-JUNB | 0.00538285 | |
MA0831.3-TFE3 | 0.00538285 | |
MA1131.1-FOSL2::JUN | 0.00538285 | |
MA1336.1-TGA3 | 0.00538285 |
Motif ID | q-val | PWM |
---|---|---|
MA1988.1-Atf3 | 6.32078e-05 | |
MA1928.1-BNC2 | 6.32078e-05 | |
MA0478.1-FOSL2 | 6.32078e-05 | |
MA0099.3-FOS::JUN | 0.00011464 | |
MA1130.1-FOSL2::JUN | 0.00011464 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.000654039 | |
MA1412.1-TSAR2 | 0.24566 | |
MA1560.1-SOHLH2 | 0.339911 | |
MA1826.1-bHLH145 | 0.339911 |
Motif ID | q-val | PWM |
---|---|---|
MA0748.2-YY2 | 7.45027e-05 | |
MA0998.1-ERF096 | 0.00019906 | |
MA1818.1-Zm00001d052229 | 0.000216057 | |
MA1651.1-ZFP42 | 0.000530575 | |
MA0997.1-ERF069 | 0.000991683 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 3.32932e-08 | |
MA0088.2-ZNF143 | 0.0221146 | |
MA1716.1-ZNF76 | 0.0431596 | |
MA0525.2-TP63 | 0.345592 | |
MA1625.1-Stat5b | 0.345592 |
Motif ID | q-val | PWM |
---|---|---|
MA0527.1-ZBTB33 | 4.48318e-07 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 4.84684e-08 | |
MA1929.1-CTCF | 2.743e-06 | |
MA1930.1-CTCF | 1.86695e-05 | |
MA0531.1-CTCF | 2.5466e-05 | |
MA1102.2-CTCFL | 4.12234e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1053.1-ERF109 | 0.00968733 | |
MA0975.1-CRF2 | 0.00968733 | |
MA0997.1-ERF069 | 0.00968733 | |
MA1820.1-Zm00001d024324 | 0.00968733 | |
MA1817.1-Zm00001d020267 | 0.00968733 |
Motif ID | q-val | PWM |
---|---|---|
MA0046.2-HNF1A | 2.60366e-05 | |
MA0153.2-HNF1B | 2.60366e-05 | |
MA0186.1-Dfd | 0.0134684 | |
MA0203.1-Scr | 0.0771914 | |
MA1198.1-HAT2 | 0.0771914 |
Motif ID | q-val | PWM |
---|---|---|
MA0375.1-RSC30 | 0.0253466 | |
MA1650.1-ZBTB14 | 0.0461101 | |
MA1834.1-Zm00001d034298 | 0.0530144 | |
MA0506.2-Nrf1 | 0.0574591 | |
MA1817.1-Zm00001d020267 | 0.0607138 |
Motif ID | q-val | PWM |
---|---|---|
MA1933.1-ELK1::SREBF2 | 0.000186821 | |
MA1939.1-ERF::SREBF2 | 0.00127576 | |
MA0765.3-ETV5 | 0.0224442 | |
MA0026.1-Eip74EF | 0.0224442 | |
MA0759.2-ELK3 | 0.0224442 |
Motif ID | q-val | PWM |
---|---|---|
MA1817.1-Zm00001d020267 | 7.11434e-06 | |
MA1820.1-Zm00001d024324 | 1.26099e-05 | |
MA1833.1-Zm00001d049364 | 1.26099e-05 | |
MA1819.1-Zm00001d005892 | 1.31765e-05 | |
MA1832.1-Zm00001d002364 | 2.29215e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 5.60403e-08 | |
MA0088.2-ZNF143 | 0.00148189 | |
MA1716.1-ZNF76 | 0.0020091 | |
MA1625.1-Stat5b | 0.170224 | |
MA0519.1-Stat5a::Stat5b | 0.326336 |
Motif ID | q-val | PWM |
---|---|---|
MA0509.3-RFX1 | 2.78342e-07 | |
MA0600.2-RFX2 | 2.78342e-07 | |
MA0798.3-RFX3 | 2.78342e-07 | |
MA0510.2-RFX5 | 2.78342e-07 | |
MA1554.1-RFX7 | 0.0326001 |
Motif ID | q-val | PWM |
---|---|---|
MA1475.1-CREB3L4 | 0.000375454 | |
MA0018.4-CREB1 | 0.000375454 | |
MA0605.2-ATF3 | 0.000533525 | |
MA1069.2-TGA6 | 0.000890161 | |
MA0656.1-JDP2 | 0.000890161 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 8.14271e-09 | |
MA1929.1-CTCF | 1.26092e-07 | |
MA1930.1-CTCF | 6.01176e-06 | |
MA1102.2-CTCFL | 0.00216035 | |
MA0531.1-CTCF | 0.0150477 |
Motif ID | q-val | PWM |
---|---|---|
MA1513.1-KLF15 | 0.000228979 | |
MA0742.2-KLF12 | 0.000484619 | |
MA0740.2-KLF14 | 0.000484619 | |
MA0516.3-SP2 | 0.000484619 | |
MA1511.2-KLF10 | 0.000484619 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.0544674 | |
MA0632.2-TCFL5 | 0.28589 | |
MA1826.1-bHLH145 | 0.28589 | |
MA1411.1-TSAR1 | 0.495726 | |
MA1412.1-TSAR2 | 0.495726 |
The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/CALU3/ENCSR935RNW/2022-07-04_06-07-54_run1_modisco/tomtom' already exists. Its contents will be overwritten. Processing query 1 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.981182 Processing query 2 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.990477 Processing query 3 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.982731 Processing query 4 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.960509 Processing query 5 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.999116 Processing query 6 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998089 Processing query 7 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 8 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 9 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.9794 Processing query 10 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.996933 Processing query 11 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.987812 Processing query 12 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 13 out of 13 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Can't locate HtmlMonolithWr.pm: /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48. Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.
Motif ID | q-val | PWM |
---|---|---|
MA1268.1-CDF5 | 0.0378524 | |
MA1884.1-Hox3 | 0.0408994 | |
MA1871.1-FoxM | 0.0408994 | |
MA1917.1-SoxC | 0.0408994 | |
MA1281.1-DOF5.1 | 0.0408994 |
Motif ID | q-val | PWM |
---|---|---|
MA1873.1-FoxQ | 0.0421883 | |
MA1867.1-FoxI-b | 0.429214 | |
MA0040.1-Foxq1 | 0.437413 | |
MA1898.1-Meox | 0.437413 | |
MA1882.1-Hnf1 | 0.437413 |
Motif ID | q-val | PWM |
---|---|---|
MA1862.1-FoxD-b | 0.0249801 | |
MA1873.1-FoxQ | 0.0249801 | |
MA1864.1-FoxF | 0.0249801 | |
MA1870.1-FoxL2 | 0.0249801 | |
MA1871.1-FoxM | 0.0249801 |
Motif ID | q-val | PWM |
---|---|---|
MA1344.1-BZIP28 | 0.236193 | |
MA0495.3-MAFF | 0.236193 | |
MA1143.1-FOSL1::JUND | 0.236193 | |
MA1172.1-MYB3R5 | 0.236193 | |
MA0492.1-JUND | 0.236193 |
Motif ID | q-val | PWM |
---|---|---|
MA1864.1-FoxF | 0.0585988 | |
MA0386.1-SPT15 | 0.136018 | |
MA1978.1-ZNF354A | 0.136018 | |
MA0379.1-MOT2 | 0.17691 | |
MA1861.1-FoxB | 0.17691 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0538.1-daf-12 | 0.000469024 |
Motif ID | q-val | PWM |
---|---|---|
MA1810.1-GLYMA-08G357600 | 0.342494 | |
MA0926.1-unc-86 | 0.394998 |
Motif ID | q-val | PWM |
---|---|---|
MA1884.1-Hox3 | 0.123548 | |
MA0681.2-PHOX2B | 0.123548 | |
MA1873.1-FoxQ | 0.123548 | |
MA1900.1-Mnx | 0.128351 | |
MA1924.1-Tlx | 0.147439 |
Motif ID | q-val | PWM |
---|---|---|
MA1864.1-FoxF | 0.161776 |
Motif ID | q-val | PWM |
---|---|---|
MA1871.1-FoxM | 8.85061e-08 | |
MA1866.1-FoxI-a | 2.60964e-05 | |
MA1281.1-DOF5.1 | 2.77899e-05 | |
MA1863.1-FoxE | 9.05754e-05 | |
MA1869.1-FoxK | 9.67521e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA0926.1-unc-86 | 0.19531 | |
MA0386.1-SPT15 | 0.326284 |
Motif ID | q-val | PWM |
---|---|---|
MA0249.2-twi | 0.301133 |