pEpiTd26 program activity among Epithelial cells

Activation of pEpiTd26
pEpiTd26 gene program activation in Epithelial cells. (Top) Activation of program across all epithelial cells. (Bottom) Activation in MMRd (left), MMRp (middle), and normal epithelial cells (right).

Epithelial cell compositional overview

Overview of epithelial cell composition
Overview of epithelial cell composition. A tSNE plot colored by: (left) MMR status of epithelial cells, (middle) specimen, (righ) epithelial cell sub-type.
Gene program activation of pEpiTd26 by different cell subtypes
pEpiTd26 gene program activation among cells of different subtypes (Epithelial cells).

pEpiTd26 top program genes

Top genes of pEpiTd26 program
Bar plots showing the top genes for each gene program, ranked by (left) unique weights, (right) raw weights.

pEpiTd26 gene-set enrichment of top program genes (using g-profiler)

GSEA wth gene profiler of pEpiTd26
pEpiTd26 gene-set enrichment summary using g-profiler webtool.
Source termID Name Padj Tsize Qsize Overlap Precision Recall
GO:BP GO:0006119 oxidative phosphorylation 0.00552612587029198 151 13 4 0.307692307692308 0.0264900662251656
GO:BP GO:0036498 IRE1-mediated unfolded protein response 0.0235477473445267 67 24 3 0.125 0.0447761194029851
GO:BP GO:0042773 ATP synthesis coupled electron transport 0.0235477473445267 100 13 3 0.230769230769231 0.03
GO:BP GO:0042775 mitochondrial ATP synthesis coupled electron transport 0.0235477473445267 99 13 3 0.230769230769231 0.0303030303030303
GO:BP GO:0022904 respiratory electron transport chain 0.0235477473445267 117 13 3 0.230769230769231 0.0256410256410256
GO:BP GO:0046034 ATP metabolic process 0.0235477473445267 314 13 4 0.307692307692308 0.0127388535031847
GO:BP GO:0045333 cellular respiration 0.0430261247741565 192 13 3 0.230769230769231 0.015625
GO:BP GO:0022900 electron transport chain 0.0430261247741565 180 13 3 0.230769230769231 0.0166666666666667
GO:CC GO:0098800 inner mitochondrial membrane protein complex 0.00337575188880727 146 7 3 0.428571428571429 0.0205479452054795
GO:CC GO:0098803 respiratory chain complex 0.00337575188880727 86 13 3 0.230769230769231 0.0348837209302326
GO:CC GO:0070469 respirasome 0.00337575188880727 103 13 3 0.230769230769231 0.029126213592233
GO:CC GO:0098798 mitochondrial protein-containing complex 0.00392850259540846 270 7 3 0.428571428571429 0.0111111111111111
GO:CC GO:0031090 organelle membrane 0.00398562301816076 3612 21 12 0.571428571428571 0.00332225913621262
GO:CC GO:0005794 Golgi apparatus 0.00398562301816076 1623 30 10 0.333333333333333 0.00616142945163278
GO:CC GO:0098796 membrane protein complex 0.00691779773794588 1322 20 7 0.35 0.00529500756429652
GO:CC GO:0005743 mitochondrial inner membrane 0.00691779773794588 503 13 4 0.307692307692308 0.00795228628230616
GO:CC GO:0098791 Golgi apparatus subcompartment 0.00765797231192964 885 30 7 0.233333333333333 0.00790960451977401
GO:CC GO:0019866 organelle inner membrane 0.00855564021525794 564 13 4 0.307692307692308 0.00709219858156028
GO:CC GO:0031984 organelle subcompartment 0.020392526606752 1773 30 9 0.3 0.0050761421319797
GO:CC GO:0031966 mitochondrial membrane 0.020392526606752 746 13 4 0.307692307692308 0.00536193029490617
GO:CC GO:0012505 endomembrane system 0.0207297689365597 4640 21 12 0.571428571428571 0.00258620689655172
GO:CC GO:0005740 mitochondrial envelope 0.022337431705993 797 13 4 0.307692307692308 0.00501882057716437
GO:CC GO:0016021 integral component of membrane 0.0314888323518397 5711 21 13 0.619047619047619 0.00227630887760462
GO:CC GO:0031967 organelle envelope 0.0320499599863315 1237 16 5 0.3125 0.00404203718674212
GO:CC GO:0031975 envelope 0.0320499599863315 1237 16 5 0.3125 0.00404203718674212
GO:CC GO:0031224 intrinsic component of membrane 0.0364521949602141 5868 21 13 0.619047619047619 0.00221540558963872
GO:CC GO:0005681 spliceosomal complex 0.0431972047099237 191 67 4 0.0597014925373134 0.0209424083769634
GO:MF GO:0009055 electron transfer activity 0.00693613504280653 148 13 3 0.230769230769231 0.0202702702702703
GO:MF GO:0016491 oxidoreductase activity 0.0433873645564172 771 13 4 0.307692307692308 0.00518806744487678
HP HP:0100611 Multiple glomerular cysts 0.000230661312493726 11 7 3 0.428571428571429 0.272727272727273
HP HP:0003572 Low plasma citrulline 0.000230661312493726 11 7 3 0.428571428571429 0.272727272727273
HP HP:0011965 Abnormal circulating citrulline concentration 0.000236697735839708 14 7 3 0.428571428571429 0.214285714285714
HP HP:0002572 Episodic vomiting 0.000236697735839708 32 13 4 0.307692307692308 0.125
HP HP:0003481 Segmental peripheral demyelination/remyelination 0.000236697735839708 17 7 3 0.428571428571429 0.176470588235294
HP HP:0003648 Lacticaciduria 0.000236697735839708 14 7 3 0.428571428571429 0.214285714285714
HP HP:0004885 Episodic respiratory distress 0.000236697735839708 17 7 3 0.428571428571429 0.176470588235294
HP HP:0000816 Abnormality of Krebs cycle metabolism 0.000236697735839708 15 7 3 0.428571428571429 0.2
HP HP:0031434 Abnormal speech prosody 0.000352017438213099 20 7 3 0.428571428571429 0.15
HP HP:0003200 Ragged-red muscle fibers 0.000441582826519918 40 13 4 0.307692307692308 0.1
HP HP:0033109 Abnormal circulating non-proteinogenic amino acid concentration 0.00044653347283252 23 7 3 0.428571428571429 0.130434782608696
HP HP:0002883 Hyperventilation 0.000674228799534215 27 7 3 0.428571428571429 0.111111111111111
HP HP:0002045 Hypothermia 0.000800545760395921 30 7 3 0.428571428571429 0.1
HP HP:0002483 Bulbar signs 0.000800545760395921 30 7 3 0.428571428571429 0.1
HP HP:0003737 Mitochondrial myopathy 0.000995947323287916 54 13 4 0.307692307692308 0.0740740740740741
HP HP:0001427 Mitochondrial inheritance 0.00114237550694486 18 13 3 0.230769230769231 0.166666666666667
HP HP:0010915 Abnormal circulating pyruvate family amino acid concentration 0.00121909454455533 38 7 3 0.428571428571429 0.0789473684210526
HP HP:0010916 Abnormal circulating alanine concentration 0.00121909454455533 38 7 3 0.428571428571429 0.0789473684210526
HP HP:0003348 Hyperalaninemia 0.00121909454455533 37 7 3 0.428571428571429 0.0810810810810811
HP HP:0007183 Focal T2 hyperintense basal ganglia lesion 0.00134747041842147 40 7 3 0.428571428571429 0.075
HP HP:0031546 Cardiac conduction abnormality 0.00134747041842147 123 14 5 0.357142857142857 0.040650406504065
HP HP:0007108 Demyelinating peripheral neuropathy 0.00142891308952238 42 7 3 0.428571428571429 0.0714285714285714
HP HP:0003800 Muscle abnormality related to mitochondrial dysfunction 0.00166078351226299 69 13 4 0.307692307692308 0.0579710144927536
HP HP:0004309 Ventricular preexcitation 0.00166078351226299 23 13 3 0.230769230769231 0.130434782608696
HP HP:0011096 Peripheral demyelination 0.00170203924681929 47 7 3 0.428571428571429 0.0638297872340425
HP HP:0033108 Abnormal circulating proteinogenic amino acid derivative concentration 0.00170203924681929 47 7 3 0.428571428571429 0.0638297872340425
HP HP:0007141 Sensorimotor neuropathy 0.00174828457837359 72 13 4 0.307692307692308 0.0555555555555556
HP HP:0012751 Abnormal basal ganglia MRI signal intensity 0.00190654539579575 50 7 3 0.428571428571429 0.06
HP HP:0001138 Optic neuropathy 0.00273513061463669 57 7 3 0.428571428571429 0.0526315789473684
HP HP:0002490 Increased CSF lactate 0.0037159213741476 91 13 4 0.307692307692308 0.043956043956044
HP HP:0030085 Abnormal CSF lactate level 0.0037159213741476 91 13 4 0.307692307692308 0.043956043956044
HP HP:0008316 Abnormal mitochondria in muscle tissue 0.00507592918912862 38 13 3 0.230769230769231 0.0789473684210526
HP HP:0000091 Abnormal renal tubule morphology 0.00592679463426331 80 7 3 0.428571428571429 0.0375
HP HP:0012072 Aciduria 0.00607428608459127 83 7 3 0.428571428571429 0.036144578313253
HP HP:0032943 Abnormal urine pH 0.00607428608459127 83 7 3 0.428571428571429 0.036144578313253
HP HP:0025454 Abnormal CSF metabolite level 0.00607428608459127 110 13 4 0.307692307692308 0.0363636363636364
HP HP:0004308 Ventricular arrhythmia 0.00607428608459127 106 24 5 0.208333333333333 0.0471698113207547
HP HP:0012469 Infantile spasms 0.00670411815097994 87 7 3 0.428571428571429 0.0344827586206897
HP HP:0000114 Proximal tubulopathy 0.00856787422467473 48 13 3 0.230769230769231 0.0625
HP HP:0003130 Abnormal peripheral myelination 0.00918430795734435 99 7 3 0.428571428571429 0.0303030303030303
HP HP:0003287 Abnormality of mitochondrial metabolism 0.0122550455168751 139 13 4 0.307692307692308 0.0287769784172662
HP HP:0001644 Dilated cardiomyopathy 0.0140295747400638 145 13 4 0.307692307692308 0.0275862068965517
HP HP:0003112 Abnormal circulating amino acid concentration 0.0140295747400638 120 7 3 0.428571428571429 0.025
HP HP:0000580 Pigmentary retinopathy 0.0155504398829038 151 13 4 0.307692307692308 0.0264900662251656
HP HP:0000095 Abnormal renal glomerulus morphology 0.0171883812466143 158 13 4 0.307692307692308 0.0253164556962025
HP HP:0031263 Abnormal renal corpuscle morphology 0.0171883812466143 158 13 4 0.307692307692308 0.0253164556962025
HP HP:0000543 Optic disc pallor 0.0187191824862431 139 7 3 0.428571428571429 0.0215827338129496
HP HP:0012103 Abnormality of the mitochondrion 0.0187191824862431 163 13 4 0.307692307692308 0.0245398773006135
HP HP:0001399 Hepatic failure 0.0194213942669108 143 7 3 0.428571428571429 0.020979020979021
HP HP:0002123 Generalized myoclonic seizure 0.0196467710721413 146 7 3 0.428571428571429 0.0205479452054795
HP HP:0002151 Increased serum lactate 0.0203417225225924 172 13 4 0.307692307692308 0.0232558139534884
HP HP:0002098 Respiratory distress 0.0263701418324102 164 7 3 0.428571428571429 0.0182926829268293
HP HP:0011035 Abnormal renal cortex morphology 0.0265751335816165 187 13 4 0.307692307692308 0.0213903743315508
HP HP:0032794 Myoclonic seizure 0.0266379254014284 167 7 3 0.428571428571429 0.0179640718562874
HP HP:0011097 Epileptic spasm 0.0272927013824631 170 7 3 0.428571428571429 0.0176470588235294
HP HP:0011344 Severe global developmental delay 0.0289046193532768 175 7 3 0.428571428571429 0.0171428571428571
HP HP:0032677 Generalized-onset motor seizure 0.0310507843273232 181 7 3 0.428571428571429 0.0165745856353591
HP HP:0002134 Abnormality of the basal ganglia 0.0310562336735959 201 13 4 0.307692307692308 0.0199004975124378
HP HP:0001410 Decreased liver function 0.0317483129315885 184 7 3 0.428571428571429 0.016304347826087
HP HP:0008947 Infantile muscular hypotonia 0.0321745580986499 188 7 3 0.428571428571429 0.0159574468085106
HP HP:0002066 Gait ataxia 0.0321745580986499 188 7 3 0.428571428571429 0.0159574468085106
HP HP:0004303 Abnormal muscle fiber morphology 0.0321745580986499 205 13 4 0.307692307692308 0.0195121951219512
HP HP:0025155 Abnormality of hepatobiliary system physiology 0.0321745580986499 188 7 3 0.428571428571429 0.0159574468085106
HP HP:0012575 Abnormal nephron morphology 0.0327543509795297 208 13 4 0.307692307692308 0.0192307692307692
HP HP:0000124 Renal tubular dysfunction 0.0369002547272921 101 13 3 0.230769230769231 0.0297029702970297
HP HP:0004354 Abnormal circulating carboxylic acid concentration 0.0438736363598052 214 7 3 0.428571428571429 0.014018691588785
HP HP:0000510 Rod-cone dystrophy 0.0438736363598052 215 7 3 0.428571428571429 0.013953488372093
HP HP:0100660 Dyskinesia 0.0482780582876144 226 7 3 0.428571428571429 0.0132743362831858
KEGG KEGG:00190 Oxidative phosphorylation 0.00334464150350415 133 13 4 0.307692307692308 0.0300751879699248
KEGG KEGG:05415 Diabetic cardiomyopathy 0.00865113824978457 203 13 4 0.307692307692308 0.0197044334975369
KEGG KEGG:04714 Thermogenesis 0.00944050204342356 232 13 4 0.307692307692308 0.0172413793103448
KEGG KEGG:05012 Parkinson disease 0.00944050204342356 249 13 4 0.307692307692308 0.0160642570281124
KEGG KEGG:05020 Prion disease 0.0106984135693444 273 13 4 0.307692307692308 0.0146520146520147
KEGG KEGG:05016 Huntington disease 0.0136854702542152 306 13 4 0.307692307692308 0.0130718954248366
KEGG KEGG:05010 Alzheimer disease 0.0205504591472706 369 13 4 0.307692307692308 0.010840108401084
KEGG KEGG:05014 Amyotrophic lateral sclerosis 0.0205504591472706 363 13 4 0.307692307692308 0.0110192837465565
KEGG KEGG:05022 Pathways of neurodegeneration - multiple diseases 0.0410742407852524 475 13 4 0.307692307692308 0.00842105263157895
MIRNA MIRNA:hsa-miR-296-3p hsa-miR-296-3p 0.0450667793896836 255 13 4 0.307692307692308 0.0156862745098039
REAC REAC:R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 0.00336204329712242 124 13 4 0.307692307692308 0.032258064516129
REAC REAC:R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 0.00638665034962316 174 13 4 0.307692307692308 0.0229885057471264
REAC REAC:R-HSA-611105 Respiratory electron transport 0.0185180057003933 100 13 3 0.230769230769231 0.03
WP WP:WP111 Electron Transport Chain (OXPHOS system in mitochondria) 0.000857709184487199 105 13 4 0.307692307692308 0.0380952380952381
WP WP:WP623 Oxidative phosphorylation 0.000857709184487199 62 7 3 0.428571428571429 0.0483870967741935

pEpiTd26 transcription factor target enrichment of top program genes

TF enrichment of pEpiTd26
Possible regulators of activation of pEpiTd26 in epithelial cells. (Left) pearson correlation of TF expression and gene expression program activatity in Epithelial cells, (right) negative log p-value for enrichment of TF binding sites among top uniqueness weighted genes for the gene program. Blue bars indicate significant TFs meeting the following criteria: FDR<0.1, overlap > 2, Corr. R > 0, permutation based p-value < 0.05.