pEpi41 program activity among Epithelial cells

Activation of pEpi41
pEpi41 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 pEpi41 by different cell subtypes
pEpi41 gene program activation among cells of different subtypes (Epithelial cells).

pEpi41 top program genes

Top genes of pEpi41 program
Bar plots showing the top genes for each gene program, ranked by (left) unique weights, (right) raw weights.

pEpi41 gene-set enrichment of top program genes (using g-profiler)

GSEA wth gene profiler of pEpi41
pEpi41 gene-set enrichment summary using g-profiler webtool.
Source termID Name Padj Tsize Qsize Overlap Precision Recall
GO:BP GO:0043413 macromolecule glycosylation 0.00125599031464589 251 40 7 0.175 0.0278884462151394
GO:BP GO:0006486 protein glycosylation 0.00125599031464589 251 40 7 0.175 0.0278884462151394
GO:BP GO:0070085 glycosylation 0.00125599031464589 264 40 7 0.175 0.0265151515151515
GO:BP GO:0016266 O-glycan processing 0.00125599031464589 58 65 5 0.0769230769230769 0.0862068965517241
GO:BP GO:0009101 glycoprotein biosynthetic process 0.00481262103493235 347 40 7 0.175 0.0201729106628242
GO:BP GO:1903729 regulation of plasma membrane organization 0.00531187226932544 14 64 3 0.046875 0.214285714285714
GO:BP GO:0023061 signal release 0.00531187226932544 496 82 11 0.134146341463415 0.0221774193548387
GO:BP GO:0006493 protein O-linked glycosylation 0.00971378599275562 102 65 5 0.0769230769230769 0.0490196078431373
GO:BP GO:0009100 glycoprotein metabolic process 0.00971378599275562 424 40 7 0.175 0.0165094339622642
GO:BP GO:0051125 regulation of actin nucleation 0.0136373426427766 31 46 3 0.0652173913043478 0.0967741935483871
GO:BP GO:0032940 secretion by cell 0.0137881547717549 1364 82 17 0.207317073170732 0.0124633431085044
GO:BP GO:0046903 secretion 0.0137881547717549 1501 82 18 0.219512195121951 0.0119920053297801
GO:BP GO:0042572 retinol metabolic process 0.0155161691363188 48 42 3 0.0714285714285714 0.0625
GO:BP GO:0120254 olefinic compound metabolic process 0.0155161691363188 121 42 4 0.0952380952380952 0.0330578512396694
GO:BP GO:0010817 regulation of hormone levels 0.0155161691363188 536 82 10 0.121951219512195 0.0186567164179104
GO:BP GO:0140352 export from cell 0.0155161691363188 1418 82 17 0.207317073170732 0.0119887165021157
GO:BP GO:0030155 regulation of cell adhesion 0.0155161691363188 748 82 12 0.146341463414634 0.0160427807486631
GO:BP GO:0140029 exocytic process 0.0160030895788998 83 63 4 0.0634920634920635 0.0481927710843374
GO:BP GO:0046503 glycerolipid catabolic process 0.0160971727953655 74 73 4 0.0547945205479452 0.0540540540540541
GO:BP GO:1901137 carbohydrate derivative biosynthetic process 0.017821128866829 686 82 11 0.134146341463415 0.0160349854227405
GO:BP GO:0034754 cellular hormone metabolic process 0.0196973639596565 140 42 4 0.0952380952380952 0.0285714285714286
GO:BP GO:0045010 actin nucleation 0.0222416626204083 57 46 3 0.0652173913043478 0.0526315789473684
GO:BP GO:1901983 regulation of protein acetylation 0.0229119565289245 78 82 4 0.0487804878048781 0.0512820512820513
GO:BP GO:0019433 triglyceride catabolic process 0.0234138477256268 38 73 3 0.0410958904109589 0.0789473684210526
GO:BP GO:0046879 hormone secretion 0.0259435941981684 317 82 7 0.0853658536585366 0.0220820189274448
GO:BP GO:0022409 positive regulation of cell-cell adhesion 0.0262801593788768 284 26 4 0.153846153846154 0.0140845070422535
GO:BP GO:0044255 cellular lipid metabolic process 0.0262801593788768 1075 42 9 0.214285714285714 0.00837209302325581
GO:BP GO:0009914 hormone transport 0.0263597076518925 327 82 7 0.0853658536585366 0.0214067278287462
GO:BP GO:0007009 plasma membrane organization 0.0293844147399735 116 66 4 0.0606060606060606 0.0344827586206897
GO:BP GO:0046461 neutral lipid catabolic process 0.0305235891783945 48 73 3 0.0410958904109589 0.0625
GO:BP GO:0046464 acylglycerol catabolic process 0.0305235891783945 48 73 3 0.0410958904109589 0.0625
GO:BP GO:0044281 small molecule metabolic process 0.0319476178676122 1921 42 12 0.285714285714286 0.0062467464862051
GO:BP GO:0001505 regulation of neurotransmitter levels 0.0322478718136165 224 63 5 0.0793650793650794 0.0223214285714286
GO:BP GO:0065008 regulation of biological quality 0.0322478718136165 4131 64 26 0.40625 0.00629387557492133
GO:BP GO:0098542 defense response to other organism 0.0331930515919039 1218 8 4 0.5 0.00328407224958949
GO:BP GO:0006629 lipid metabolic process 0.0333462778421906 1457 55 12 0.218181818181818 0.00823610157858614
GO:BP GO:1901985 positive regulation of protein acetylation 0.0333462778421906 46 82 3 0.0365853658536585 0.0652173913043478
GO:BP GO:0034308 primary alcohol metabolic process 0.0348050508801688 95 42 3 0.0714285714285714 0.0315789473684211
GO:BP GO:0006024 glycosaminoglycan biosynthetic process 0.0348050508801688 107 82 4 0.0487804878048781 0.0373831775700935
GO:BP GO:0032879 regulation of localization 0.0362093039688586 2872 82 24 0.292682926829268 0.00835654596100279
GO:BP GO:0048278 vesicle docking 0.0371825995939546 67 63 3 0.0476190476190476 0.0447761194029851
GO:BP GO:0033036 macromolecule localization 0.0371825995939546 3218 70 23 0.328571428571429 0.00714729645742697
GO:BP GO:0050796 regulation of insulin secretion 0.0372576403195002 189 82 5 0.0609756097560976 0.0264550264550265
GO:BP GO:0042445 hormone metabolic process 0.0388046717149419 228 42 4 0.0952380952380952 0.0175438596491228
GO:BP GO:0006023 aminoglycan biosynthetic process 0.0388046717149419 114 82 4 0.0487804878048781 0.0350877192982456
GO:BP GO:1903510 mucopolysaccharide metabolic process 0.0389115467975871 116 82 4 0.0487804878048781 0.0344827586206897
GO:BP GO:0001523 retinoid metabolic process 0.0391795072044345 107 42 3 0.0714285714285714 0.0280373831775701
GO:BP GO:0035065 regulation of histone acetylation 0.0395468551273443 55 82 3 0.0365853658536585 0.0545454545454545
GO:BP GO:0006887 exocytosis 0.0412642325121055 904 69 10 0.144927536231884 0.0110619469026549
GO:BP GO:0032418 lysosome localization 0.0412642325121055 76 61 3 0.0491803278688525 0.0394736842105263
GO:BP GO:0006721 terpenoid metabolic process 0.0423045657769926 123 42 3 0.0714285714285714 0.024390243902439
GO:BP GO:0051707 response to other organism 0.0423045657769926 1592 4 3 0.75 0.00188442211055276
GO:BP GO:2000756 regulation of peptidyl-lysine acetylation 0.0423045657769926 63 82 3 0.0365853658536585 0.0476190476190476
GO:BP GO:0051046 regulation of secretion 0.0423045657769926 647 82 9 0.109756097560976 0.0139103554868624
GO:BP GO:0051640 organelle localization 0.0423045657769926 668 64 8 0.125 0.0119760479041916
GO:BP GO:0009607 response to biotic stimulus 0.0423045657769926 1626 4 3 0.75 0.0018450184501845
GO:BP GO:0097006 regulation of plasma lipoprotein particle levels 0.0423045657769926 107 47 3 0.0638297872340425 0.0280373831775701
GO:BP GO:0030838 positive regulation of actin filament polymerization 0.0423045657769926 104 46 3 0.0652173913043478 0.0288461538461538
GO:BP GO:0097193 intrinsic apoptotic signaling pathway 0.0423045657769926 294 36 4 0.111111111111111 0.0136054421768707
GO:BP GO:0016101 diterpenoid metabolic process 0.0423045657769926 113 42 3 0.0714285714285714 0.0265486725663717
GO:BP GO:0043207 response to external biotic stimulus 0.0423045657769926 1594 4 3 0.75 0.00188205771643664
GO:BP GO:0051179 localization 0.0423045657769926 6901 64 36 0.5625 0.00521663527025069
GO:BP GO:0090276 regulation of peptide hormone secretion 0.0425374538167522 221 82 5 0.0609756097560976 0.0226244343891403
GO:BP GO:0030073 insulin secretion 0.0425374538167522 218 82 5 0.0609756097560976 0.0229357798165138
GO:BP GO:0007155 cell adhesion 0.0425374538167522 1492 19 6 0.315789473684211 0.00402144772117962
GO:BP GO:0045785 positive regulation of cell adhesion 0.0425374538167522 437 26 4 0.153846153846154 0.0091533180778032
GO:BP GO:0046888 negative regulation of hormone secretion 0.0425374538167522 66 82 3 0.0365853658536585 0.0454545454545455
GO:BP GO:0022610 biological adhesion 0.0425945841736124 1499 19 6 0.315789473684211 0.00400266844563042
GO:BP GO:0010950 positive regulation of endopeptidase activity 0.0428358630635683 187 60 4 0.0666666666666667 0.0213903743315508
GO:BP GO:0034613 cellular protein localization 0.0428358630635683 2014 82 18 0.219512195121951 0.00893743793445879
GO:BP GO:0022407 regulation of cell-cell adhesion 0.0432436030334462 445 26 4 0.153846153846154 0.00898876404494382
GO:BP GO:0006952 defense response 0.0438128282467186 1818 4 3 0.75 0.00165016501650165
GO:BP GO:0070727 cellular macromolecule localization 0.0438128282467186 2024 82 18 0.219512195121951 0.00889328063241107
GO:BP GO:0006643 membrane lipid metabolic process 0.0456983498089758 217 55 4 0.0727272727272727 0.0184331797235023
GO:BP GO:1903827 regulation of cellular protein localization 0.0456983498089758 572 82 8 0.0975609756097561 0.013986013986014
GO:BP GO:0051235 maintenance of location 0.0456983498089758 337 82 6 0.0731707317073171 0.0178041543026706
GO:BP GO:0006720 isoprenoid metabolic process 0.046337241446082 144 42 3 0.0714285714285714 0.0208333333333333
GO:BP GO:0010952 positive regulation of peptidase activity 0.0480073405008684 205 60 4 0.0666666666666667 0.0195121951219512
GO:BP GO:1903039 positive regulation of leukocyte cell-cell adhesion 0.0485649433540918 241 26 3 0.115384615384615 0.012448132780083
GO:BP GO:0060341 regulation of cellular localization 0.0496518543520181 851 82 10 0.121951219512195 0.0117508813160987
GO:CC GO:1903561 extracellular vesicle 5.72814792267835e-06 2261 46 20 0.434782608695652 0.00884564352056612
GO:CC GO:0070062 extracellular exosome 5.72814792267835e-06 2176 46 20 0.434782608695652 0.00919117647058824
GO:CC GO:0043230 extracellular organelle 5.72814792267835e-06 2263 46 20 0.434782608695652 0.00883782589482987
GO:CC GO:0012505 endomembrane system 5.72814792267835e-06 4640 70 39 0.557142857142857 0.0084051724137931
GO:CC GO:0031985 Golgi cisterna 6.75144245683477e-06 115 40 6 0.15 0.0521739130434783
GO:CC GO:0031982 vesicle 8.67415151731696e-06 4055 72 35 0.486111111111111 0.00863131935881628
GO:CC GO:0005615 extracellular space 8.67415151731696e-06 3594 48 25 0.520833333333333 0.00695603784084585
GO:CC GO:0005576 extracellular region 8.67415151731696e-06 4567 40 25 0.625 0.00547405298883293
GO:CC GO:0031224 intrinsic component of membrane 8.69282501131649e-06 5868 67 41 0.611940298507463 0.00698704839809134
GO:CC GO:0098588 bounding membrane of organelle 8.74425872173091e-06 2158 65 23 0.353846153846154 0.0106580166821131
GO:CC GO:0016021 integral component of membrane 1.15584917285957e-05 5711 67 40 0.597014925373134 0.00700402731570653
GO:CC GO:0005795 Golgi stack 1.44237912989823e-05 149 40 6 0.15 0.0402684563758389
GO:CC GO:0031090 organelle membrane 9.26946218578211e-05 3612 67 29 0.432835820895522 0.00802879291251384
GO:CC GO:0031984 organelle subcompartment 0.00014547044201549 1773 67 19 0.283582089552239 0.0107163000564016
GO:CC GO:0000139 Golgi membrane 0.000185966674781184 771 65 12 0.184615384615385 0.0155642023346304
GO:CC GO:0005794 Golgi apparatus 0.000288549216765925 1623 70 18 0.257142857142857 0.011090573012939
GO:CC GO:0016020 membrane 0.000567651914254076 9838 70 53 0.757142857142857 0.00538727383614556
GO:CC GO:0032580 Golgi cisterna membrane 0.000573047331276802 90 40 4 0.1 0.0444444444444444
GO:CC GO:0098791 Golgi apparatus subcompartment 0.000581790536679084 885 65 12 0.184615384615385 0.0135593220338983
GO:CC GO:0031410 cytoplasmic vesicle 0.000794464273134637 2424 72 22 0.305555555555556 0.00907590759075908
GO:CC GO:0097708 intracellular vesicle 0.000794464273134637 2428 72 22 0.305555555555556 0.00906095551894563
GO:CC GO:0005737 cytoplasm 0.00218825110762413 11911 47 41 0.872340425531915 0.00344219628914449
GO:CC GO:0099503 secretory vesicle 0.00299870831290633 1020 69 12 0.173913043478261 0.0117647058823529
GO:CC GO:0030139 endocytic vesicle 0.00332331063823018 306 9 3 0.333333333333333 0.00980392156862745
GO:CC GO:0071944 cell periphery 0.00510389185308325 6169 64 34 0.53125 0.00551142810828335
GO:CC GO:0005796 Golgi lumen 0.00566097021368046 99 32 3 0.09375 0.0303030303030303
GO:CC GO:0005886 plasma membrane 0.00566097021368046 5681 64 32 0.5 0.00563281112480197
GO:CC GO:0000323 lytic vacuole 0.008465263197817 712 82 10 0.121951219512195 0.0140449438202247
GO:CC GO:0005764 lysosome 0.008465263197817 712 82 10 0.121951219512195 0.0140449438202247
GO:CC GO:0030141 secretory granule 0.00889307502767916 851 27 6 0.222222222222222 0.00705052878965922
GO:CC GO:0031983 vesicle lumen 0.0116793155185748 326 14 3 0.214285714285714 0.00920245398773006
GO:CC GO:0060205 cytoplasmic vesicle lumen 0.0116793155185748 324 14 3 0.214285714285714 0.00925925925925926
GO:CC GO:0098852 lytic vacuole membrane 0.0120220889436903 383 26 4 0.153846153846154 0.010443864229765
GO:CC GO:0005765 lysosomal membrane 0.0120220889436903 383 26 4 0.153846153846154 0.010443864229765
GO:CC GO:0030670 phagocytic vesicle membrane 0.0143896781657193 76 64 3 0.046875 0.0394736842105263
GO:CC GO:0005773 vacuole 0.0161370246698244 810 82 10 0.121951219512195 0.0123456790123457
GO:CC GO:0005774 vacuolar membrane 0.0172607503144718 441 26 4 0.153846153846154 0.0090702947845805
GO:CC GO:0016324 apical plasma membrane 0.0172607503144718 361 32 4 0.125 0.0110803324099723
GO:CC GO:0005925 focal adhesion 0.0172607503144718 420 64 6 0.09375 0.0142857142857143
GO:CC GO:0042175 nuclear outer membrane-endoplasmic reticulum membrane network 0.0172607503144718 1139 42 8 0.19047619047619 0.00702370500438982
GO:CC GO:0030055 cell-substrate junction 0.0172607503144718 427 64 6 0.09375 0.0140515222482436
GO:CC GO:0010008 endosome membrane 0.0179590123483011 505 55 6 0.109090909090909 0.0118811881188119
GO:CC GO:0030133 transport vesicle 0.0194809923341425 414 69 6 0.0869565217391304 0.0144927536231884
GO:CC GO:0048471 perinuclear region of cytoplasm 0.0200799918859523 735 40 6 0.15 0.00816326530612245
GO:CC GO:0045177 apical part of cell 0.0259774659729365 431 32 4 0.125 0.00928074245939675
GO:CC GO:0070161 anchoring junction 0.0296575456913071 836 51 7 0.137254901960784 0.00837320574162679
GO:CC GO:0030054 cell junction 0.0370399792565015 2105 64 14 0.21875 0.00665083135391924
GO:CC GO:0070382 exocytic vesicle 0.0370399792565015 229 69 4 0.0579710144927536 0.0174672489082969
GO:CC GO:0005768 endosome 0.0377279051282908 987 70 9 0.128571428571429 0.00911854103343465
GO:CC GO:0005938 cell cortex 0.0381906185368011 311 81 5 0.0617283950617284 0.0160771704180064
GO:CC GO:0005789 endoplasmic reticulum membrane 0.0381906185368011 1117 42 7 0.166666666666667 0.0062667860340197
GO:CC GO:0098827 endoplasmic reticulum subcompartment 0.0385287591063528 1122 42 7 0.166666666666667 0.00623885918003565
GO:CC GO:0042581 specific granule 0.0424953219912131 158 61 3 0.0491803278688525 0.0189873417721519
GO:CC GO:0005766 primary lysosome 0.0424953219912131 154 61 3 0.0491803278688525 0.0194805194805195
GO:CC GO:0030667 secretory granule membrane 0.0424953219912131 303 58 4 0.0689655172413793 0.0132013201320132
GO:CC GO:0042582 azurophil granule 0.0424953219912131 154 61 3 0.0491803278688525 0.0194805194805195
GO:CC GO:0070820 tertiary granule 0.0450657557356937 163 61 3 0.0491803278688525 0.0184049079754601
GO:CC GO:0030666 endocytic vesicle membrane 0.0468641186350416 159 64 3 0.046875 0.0188679245283019
GO:MF GO:0042043 neurexin family protein binding 0.00778610407371869 15 69 3 0.0434782608695652 0.2
GO:MF GO:0051015 actin filament binding 0.0206182894602191 212 46 4 0.0869565217391304 0.0188679245283019
GO:MF GO:0016758 transferase activity, transferring hexosyl groups 0.0206182894602191 205 72 5 0.0694444444444444 0.024390243902439
GO:MF GO:0016757 transferase activity, transferring glycosyl groups 0.0206182894602191 283 72 6 0.0833333333333333 0.0212014134275618
GO:MF GO:0016298 lipase activity 0.0206182894602191 134 73 4 0.0547945205479452 0.0298507462686567
GO:MF GO:0052689 carboxylic ester hydrolase activity 0.0229432322166406 146 73 4 0.0547945205479452 0.0273972602739726
GO:MF GO:0005102 signaling receptor binding 0.031721005019316 1672 13 5 0.384615384615385 0.00299043062200957
GO:MF GO:0003779 actin binding 0.0332268573516129 448 46 5 0.108695652173913 0.0111607142857143
GO:MF GO:0000149 SNARE binding 0.0387899284242147 114 63 3 0.0476190476190476 0.0263157894736842
GO:MF GO:0005543 phospholipid binding 0.0387899284242147 454 69 6 0.0869565217391304 0.013215859030837
GO:MF GO:0043177 organic acid binding 0.0387899284242147 120 60 3 0.05 0.025
GO:MF GO:0005509 calcium ion binding 0.0435870557217386 721 46 6 0.130434782608696 0.00832177531206657
GO:MF GO:0004620 phospholipase activity 0.0456870056580529 109 73 3 0.0410958904109589 0.0275229357798165
GO:MF GO:0016787 hydrolase activity 0.0475801260061134 2615 47 13 0.276595744680851 0.00497131931166348
KEGG KEGG:00601 Glycosphingolipid biosynthesis - lacto and neolacto series 0.0330591868423816 27 37 3 0.0810810810810811 0.111111111111111
REAC REAC:R-HSA-9033658 Blood group systems biosynthesis 0.00257393040883715 21 37 3 0.0810810810810811 0.142857142857143
REAC REAC:R-HSA-913709 O-linked glycosylation of mucins 0.00257393040883715 61 65 5 0.0769230769230769 0.0819672131147541
REAC REAC:R-HSA-5083625 Defective GALNT3 causes familial hyperphosphatemic tumoral calcinosis (HFTC) 0.00257393040883715 16 40 3 0.075 0.1875
REAC REAC:R-HSA-977068 Termination of O-glycan biosynthesis 0.00257393040883715 23 32 3 0.09375 0.130434782608696
REAC REAC:R-HSA-9037629 Lewis blood group biosynthesis 0.00257393040883715 18 37 3 0.0810810810810811 0.166666666666667
REAC REAC:R-HSA-5173105 O-linked glycosylation 0.0163087544379722 107 65 5 0.0769230769230769 0.0467289719626168
REAC REAC:R-HSA-1483206 Glycerophospholipid biosynthesis 0.0275335022560663 128 41 4 0.0975609756097561 0.03125
REAC REAC:R-HSA-3781865 Diseases of glycosylation 0.0298231891146362 140 40 4 0.1 0.0285714285714286
REAC REAC:R-HSA-3906995 Diseases associated with O-glycosylation of proteins 0.0298231891146362 65 40 3 0.075 0.0461538461538462
REAC REAC:R-HSA-5668914 Diseases of metabolism 0.0306336447033121 241 40 5 0.125 0.020746887966805
REAC REAC:R-HSA-71387 Metabolism of carbohydrates 0.0371415473141756 285 72 7 0.0972222222222222 0.0245614035087719
TF TF:M09916_1 Factor: Erm; motif: NRRSAGGAARNGRN; match class: 1 0.0359562641409432 1643 44 14 0.318181818181818 0.00852099817407182
TF TF:M04457_1 Factor: ESRRA; motif: AAGGTCATNCAAGGTCA; match class: 1 0.0359562641409432 389 19 5 0.263157894736842 0.012853470437018
TF TF:M08964_1 Factor: NR1B1:RXR-ALPHA; motif: RRGGTCANNNNNRGGTCA; match class: 1 0.0359562641409432 1827 29 11 0.379310344827586 0.0060207991242474
TF TF:M06916 Factor: ZNF652; motif: NATSGGGCTC 0.0359562641409432 43 71 4 0.0563380281690141 0.0930232558139535
TF TF:M11819_1 Factor: T3R-beta; motif: RTGACCTYACRTGACCTYA; match class: 1 0.0359562641409432 1613 27 10 0.37037037037037 0.00619962802231866
TF TF:M03582_1 Factor: TWIST; motif: CACCTGG; match class: 1 0.0370423140696631 2579 83 25 0.301204819277108 0.00969367972082202
WP WP:WP2291 Deregulation of Rab and Rab Effector Genes in Bladder Cancer 0.00103242438584473 16 69 4 0.0579710144927536 0.25

pEpi41 transcription factor target enrichment of top program genes

TF enrichment of pEpi41
Possible regulators of activation of pEpi41 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.