# 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("2022-07-02_16-51-15_run1_modisco_config_A673_profile.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/A673/ENCSR046BCI/2022-07-02_16-51-15_run1_modisco cell_type: A673 ENCSR046BCI timestamp: 2022-07-02_16-51-15 run: 1 scoring_type: profile 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_slice" + str(score_center_size) + ".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_slice" + str(score_center_size) + ".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 [00:18<00:00, 1.31it/s] Loading Peaks: 44667it [01:16, 581.35it/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)
18595 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
8050 seqlets
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4297 seqlets
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4008 seqlets
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3640 seqlets
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2803 seqlets
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2737 seqlets
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2614 seqlets
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2352 seqlets
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2108 seqlets
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1728 seqlets
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1343 seqlets
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1135 seqlets
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1082 seqlets
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1004 seqlets
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828 seqlets
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707 seqlets
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691 seqlets
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672 seqlets
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623 seqlets
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571 seqlets
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561 seqlets
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489 seqlets
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462 seqlets
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133 seqlets
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112 seqlets
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92 seqlets
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92 seqlets
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76 seqlets
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61 seqlets
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49 seqlets
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45 seqlets
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42 seqlets
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30 seqlets
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25 seqlets
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24 seqlets
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22 seqlets
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21 seqlets
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20 seqlets
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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/A673/ENCSR046BCI/2022-07-02_16-51-15_run1_modisco/tomtom' already exists. Its contents will be overwritten. Processing query 1 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 2 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 3 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.973436 Processing query 4 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 5 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.984472 Processing query 6 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.9613 Processing query 7 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 8 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.959039 Processing query 9 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.958135 Processing query 10 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.951707 Processing query 11 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.995125 Processing query 12 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 13 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.984472 Processing query 14 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.976018 Processing query 15 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.967175 Processing query 16 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 17 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.983959 Processing query 18 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.994235 Processing query 19 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.990834 Processing query 20 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.989186 Processing query 21 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 22 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 23 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 24 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.964623 Processing query 25 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.983506 Processing query 26 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.999887 Processing query 27 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.985266 Processing query 28 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 29 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 30 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.962674 Processing query 31 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.957999 Processing query 32 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 33 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 34 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 35 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.977891 Processing query 36 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 37 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 38 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.976301 Processing query 39 out of 39 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998859 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.
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0742.2-KLF12 | 0.000252255 | |
MA0741.1-KLF16 | 0.000252255 | |
MA0516.3-SP2 | 0.000252255 | |
MA0685.2-SP4 | 0.000252255 | |
MA0740.2-KLF14 | 0.000252255 |
Motif ID | q-val | PWM |
---|---|---|
MA0060.3-NFYA | 2.51299e-05 | |
MA1644.1-NFYC | 2.64446e-05 | |
MA0316.1-HAP5 | 4.90769e-05 | |
MA0314.2-HAP3 | 5.59358e-05 | |
MA0502.2-NFYB | 0.0522209 |
Motif ID | q-val | PWM |
---|---|---|
MA0076.2-ELK4 | 4.44668e-07 | |
MA0764.3-ETV4 | 1.09452e-05 | |
MA0026.1-Eip74EF | 1.09452e-05 | |
MA0759.2-ELK3 | 1.33697e-05 | |
MA0916.1-Ets21C | 1.33697e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1262.1-ERF2 | 1.81657e-08 | |
MA1833.1-Zm00001d049364 | 1.81657e-08 | |
MA1239.1-ERF104 | 1.81657e-08 | |
MA1257.1-ERF9 | 1.81657e-08 | |
MA2022.1-LOB | 3.06319e-08 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA1475.1-CREB3L4 | 0.000831646 | |
MA1438.1-atf-7 | 0.00206474 | |
MA0609.2-CREM | 0.00212293 | |
MA1346.1-TGA10 | 0.00214058 | |
MA1348.1-TGA9 | 0.00214058 |
Motif ID | q-val | PWM |
---|---|---|
MA0975.1-CRF2 | 4.61962e-05 | |
MA1832.1-Zm00001d002364 | 4.61962e-05 | |
MA1821.1-Zm00001d020595 | 5.25831e-05 | |
MA1818.1-Zm00001d052229 | 0.000120409 | |
MA1819.1-Zm00001d005892 | 0.000128627 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 1.70031e-09 | |
MA1832.1-Zm00001d002364 | 2.55945e-08 | |
MA1821.1-Zm00001d020595 | 2.55945e-08 | |
MA1820.1-Zm00001d024324 | 1.19751e-07 | |
MA1817.1-Zm00001d020267 | 1.34795e-07 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.000113552 | |
MA1816.1-O11 | 0.186743 | |
MA1826.1-bHLH145 | 0.186743 | |
MA1412.1-TSAR2 | 0.194313 | |
MA0162.4-EGR1 | 0.258007 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA1988.1-Atf3 | 2.2491e-06 | |
MA1138.1-FOSL2::JUNB | 3.52897e-05 | |
MA1135.1-FOSB::JUNB | 3.52897e-05 | |
MA0478.1-FOSL2 | 3.52897e-05 | |
MA0462.2-BATF::JUN | 3.52897e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1513.1-KLF15 | 0.00711036 | |
MA0742.2-KLF12 | 0.0134497 | |
MA1511.2-KLF10 | 0.0134497 | |
MA1818.1-Zm00001d052229 | 0.0134497 | |
MA0079.5-SP1 | 0.0134497 |
Motif ID | q-val | PWM |
---|---|---|
MA0975.1-CRF2 | 7.05631e-05 | |
MA1817.1-Zm00001d020267 | 7.05631e-05 | |
MA1833.1-Zm00001d049364 | 8.0821e-05 | |
MA0748.2-YY2 | 8.0821e-05 | |
MA1819.1-Zm00001d005892 | 8.78028e-05 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA1890.1-Klf15 | 3.52067e-07 | |
MA1893.1-Klf6-7-like | 9.99741e-06 | |
MA1892.1-Klf5-like | 1.02813e-05 | |
MA1513.1-KLF15 | 0.000407421 | |
MA1961.1-PATZ1 | 0.000483413 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 2.7991e-10 | |
MA1929.1-CTCF | 2.7991e-10 | |
MA1930.1-CTCF | 4.5977e-09 | |
MA1102.2-CTCFL | 1.32631e-05 | |
MA0531.1-CTCF | 4.6824e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1109.1-NEUROD1 | 0.423686 | |
MA0373.1-RPN4 | 0.423686 | |
MA1467.2-Atoh1 | 0.423686 | |
MA0813.1-TFAP2B | 0.423686 | |
MA1257.1-ERF9 | 0.423686 |
Motif ID | q-val | PWM |
---|---|---|
MA0833.2-ATF4 | 3.15106e-06 | |
MA1636.1-CEBPG | 0.000123352 | |
MA0488.1-JUN | 0.0310915 | |
MA0025.2-NFIL3 | 0.0310915 | |
MA1702.1-Pdp1 | 0.0310915 |
Motif ID | q-val | PWM |
---|---|---|
MA0080.6-Spi1 | 0.456298 | |
MA1823.1-Zm00001d027846 | 0.456298 | |
MA0452.2-Kr | 0.456298 | |
MA0277.1-AZF1 | 0.456298 | |
MA0687.1-SPIC | 0.494966 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 6.62891e-09 | |
MA0088.2-ZNF143 | 0.0640494 | |
MA1716.1-ZNF76 | 0.0666309 |
Motif ID | q-val | PWM |
---|---|---|
MA0527.1-ZBTB33 | 0.000340075 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.000246672 | |
MA1820.1-Zm00001d024324 | 0.000246672 | |
MA1817.1-Zm00001d020267 | 0.000246672 | |
MA1961.1-PATZ1 | 0.000246672 | |
MA1713.1-ZNF610 | 0.000246672 |
Motif ID | q-val | PWM |
---|---|---|
MA1723.1-PRDM9 | 0.00101382 | |
MA0528.2-ZNF263 | 0.0280506 | |
MA1240.1-ERF10 | 0.0291076 | |
MA1945.1-ETV5::FIGLA | 0.0370855 | |
MA1403.1-BPC5 | 0.0370855 |
Motif ID | q-val | PWM |
---|---|---|
MA0088.2-ZNF143 | 0.00189837 | |
MA1716.1-ZNF76 | 0.00189837 | |
MA1573.2-Thap11 | 0.00265745 | |
MA0519.1-Stat5a::Stat5b | 0.0833267 | |
MA1116.1-RBPJ | 0.220687 |
Motif ID | q-val | PWM |
---|---|---|
MA1266.1-RAP2-11 | 0.49816 | |
MA1671.1-ERF118 | 0.49816 | |
MA1132.1-JUN::JUNB | 0.49816 | |
MA1976.1-ZNF320 | 0.49816 | |
MA1222.1-ERF014 | 0.49816 |
Motif ID | q-val | PWM |
---|---|---|
MA0332.1-MET28 | 0.110508 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.000217505 | |
MA1880.1-Hey | 0.00303091 | |
MA1833.1-Zm00001d049364 | 0.0115421 | |
MA1826.1-bHLH145 | 0.0449299 | |
MA1817.1-Zm00001d020267 | 0.0852408 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.000109697 | |
MA1817.1-Zm00001d020267 | 0.000383482 | |
MA1819.1-Zm00001d005892 | 0.000504604 | |
MA1832.1-Zm00001d002364 | 0.000566964 | |
MA1821.1-Zm00001d020595 | 0.000566964 |
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 3.16775e-07 |
Motif ID | q-val | PWM |
---|---|---|
MA1713.1-ZNF610 | 0.00749135 | |
MA1513.1-KLF15 | 0.172566 | |
MA1522.1-MAZ | 0.172566 | |
MA1430.1-TB1 | 0.172566 | |
MA1820.1-Zm00001d024324 | 0.172566 |
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA1716.1-ZNF76 | 0.00748542 | |
MA1513.1-KLF15 | 0.0283549 | |
MA1687.1-ARF14 | 0.0283549 | |
MA1961.1-PATZ1 | 0.0283549 | |
MA1899.1-Mitf | 0.0669486 |
Motif ID | q-val | PWM |
---|---|---|
MA1716.1-ZNF76 | 0.156527 | |
MA1687.1-ARF14 | 0.156527 | |
MA1673.1-LBD18 | 0.156527 | |
MA1573.2-Thap11 | 0.156527 | |
MA1285.1-TCP9 | 0.341251 |