pEpi14 program activity among Epithelial cells

Activation of pEpi14
pEpi14 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 pEpi14 by different cell subtypes
pEpi14 gene program activation among cells of different subtypes (Epithelial cells).

pEpi14 top program genes

Top genes of pEpi14 program
Bar plots showing the top genes for each gene program, ranked by (left) unique weights, (right) raw weights.

pEpi14 gene-set enrichment of top program genes (using g-profiler)

GSEA wth gene profiler of pEpi14
pEpi14 gene-set enrichment summary using g-profiler webtool.
Source termID Name Padj Tsize Qsize Overlap Precision Recall
GO:BP GO:0044278 cell wall disruption in other organism 8.75959527894717e-09 4 3 3 1 0.75
GO:BP GO:0006959 humoral immune response 2.24387378238768e-07 384 10 7 0.7 0.0182291666666667
GO:BP GO:0019730 antimicrobial humoral response 4.59544357692926e-07 145 7 5 0.714285714285714 0.0344827586206897
GO:BP GO:0006953 acute-phase response 2.03458160619163e-06 50 89 7 0.0786516853932584 0.14
GO:BP GO:0002526 acute inflammatory response 2.03458160619163e-06 114 89 9 0.101123595505618 0.0789473684210526
GO:BP GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide 3.11403612166571e-05 81 3 3 1 0.037037037037037
GO:BP GO:0035821 modulation of process of other organism 0.000106796985640924 128 3 3 1 0.0234375
GO:BP GO:0051707 response to other organism 0.000918724826439679 1592 10 7 0.7 0.00439698492462312
GO:BP GO:0043207 response to external biotic stimulus 0.000918724826439679 1594 10 7 0.7 0.00439146800501882
GO:BP GO:0009607 response to biotic stimulus 0.00094577790491426 1626 10 7 0.7 0.0043050430504305
GO:BP GO:0006954 inflammatory response 0.00135075239456099 794 89 15 0.168539325842697 0.0188916876574307
GO:BP GO:0043434 response to peptide hormone 0.00297983547216088 462 3 3 1 0.00649350649350649
GO:BP GO:0050830 defense response to Gram-positive bacterium 0.00433741918677805 101 63 5 0.0793650793650794 0.0495049504950495
GO:BP GO:1901652 response to peptide 0.00433741918677805 551 3 3 1 0.00544464609800363
GO:BP GO:0042742 defense response to bacterium 0.00460680788550353 349 67 8 0.119402985074627 0.0229226361031519
GO:BP GO:0006955 immune response 0.00460680788550353 2311 10 7 0.7 0.00302899177845089
GO:BP GO:0045995 regulation of embryonic development 0.00460680788550353 63 21 3 0.142857142857143 0.0476190476190476
GO:BP GO:0044419 biological process involved in interspecies interaction between organisms 0.00460680788550353 2255 10 7 0.7 0.00310421286031042
GO:BP GO:0009605 response to external stimulus 0.00839053663851787 2944 27 13 0.481481481481481 0.00441576086956522
GO:BP GO:0009725 response to hormone 0.00947358843020161 921 3 3 1 0.00325732899022801
GO:BP GO:0006952 defense response 0.0103197947175024 1818 89 21 0.235955056179775 0.0115511551155116
GO:BP GO:0008284 positive regulation of cell population proliferation 0.0104415610031657 982 3 3 1 0.00305498981670061
GO:BP GO:0010837 regulation of keratinocyte proliferation 0.0124338666822228 39 53 3 0.0566037735849057 0.0769230769230769
GO:BP GO:0010243 response to organonitrogen compound 0.0129139105947518 1085 3 3 1 0.00276497695852535
GO:BP GO:0009617 response to bacterium 0.013429116384261 743 75 11 0.146666666666667 0.0148048452220727
GO:BP GO:1901698 response to nitrogen compound 0.0142941821147209 1172 3 3 1 0.00255972696245734
GO:BP GO:0002376 immune system process 0.0145280947516046 3278 12 8 0.666666666666667 0.0024405125076266
GO:BP GO:0050829 defense response to Gram-negative bacterium 0.015917232117308 88 67 4 0.0597014925373134 0.0454545454545455
GO:BP GO:0002675 positive regulation of acute inflammatory response 0.0172194277833513 29 87 3 0.0344827586206897 0.103448275862069
GO:BP GO:0043616 keratinocyte proliferation 0.019834105487405 50 53 3 0.0566037735849057 0.06
GO:BP GO:0050673 epithelial cell proliferation 0.0227883736218529 460 56 7 0.125 0.0152173913043478
GO:BP GO:0030449 regulation of complement activation 0.0248615420267135 110 27 3 0.111111111111111 0.0272727272727273
GO:BP GO:0050896 response to stimulus 0.0271726119073839 9407 46 35 0.760869565217391 0.00372063357074519
GO:BP GO:0008283 cell population proliferation 0.0271726119073839 2054 19 8 0.421052631578947 0.00389483933787731
GO:BP GO:0045616 regulation of keratinocyte differentiation 0.0277249383214701 43 73 3 0.0410958904109589 0.0697674418604651
GO:BP GO:0042127 regulation of cell population proliferation 0.0299448834065193 1774 56 14 0.25 0.00789177001127396
GO:BP GO:0009719 response to endogenous stimulus 0.0299448834065193 1683 3 3 1 0.0017825311942959
GO:BP GO:1901700 response to oxygen-containing compound 0.0324765554109302 1739 3 3 1 0.00172512938470385
GO:BP GO:0042060 wound healing 0.032718671662134 549 83 9 0.108433734939759 0.0163934426229508
GO:BP GO:0009611 response to wounding 0.0341301085702194 674 83 10 0.120481927710843 0.0148367952522255
GO:BP GO:0002920 regulation of humoral immune response 0.0341301085702194 133 27 3 0.111111111111111 0.0225563909774436
GO:BP GO:0006958 complement activation, classical pathway 0.0352275343334209 142 27 3 0.111111111111111 0.0211267605633803
GO:BP GO:0010033 response to organic substance 0.0353188604554684 3412 4 4 1 0.00117233294255569
GO:BP GO:0002455 humoral immune response mediated by circulating immunoglobulin 0.0406586050965503 156 27 3 0.111111111111111 0.0192307692307692
GO:BP GO:0002673 regulation of acute inflammatory response 0.0438939964016447 50 87 3 0.0344827586206897 0.06
GO:BP GO:0045604 regulation of epidermal cell differentiation 0.0473734182299414 63 73 3 0.0410958904109589 0.0476190476190476
GO:CC GO:0005576 extracellular region 9.75803188186204e-06 4567 73 39 0.534246575342466 0.00853952266257937
GO:CC GO:0005615 extracellular space 9.75803188186204e-06 3594 73 34 0.465753424657534 0.00946021146355036
GO:CC GO:0043230 extracellular organelle 0.000219630714793287 2263 11 8 0.727272727272727 0.00353513035793195
GO:CC GO:0070062 extracellular exosome 0.000219630714793287 2176 11 8 0.727272727272727 0.00367647058823529
GO:CC GO:1903561 extracellular vesicle 0.000219630714793287 2261 11 8 0.727272727272727 0.00353825740822645
GO:CC GO:0031012 extracellular matrix 0.000475940253246927 562 90 12 0.133333333333333 0.0213523131672598
GO:CC GO:0030312 external encapsulating structure 0.000475940253246927 563 90 12 0.133333333333333 0.0213143872113677
GO:CC GO:0062023 collagen-containing extracellular matrix 0.000848884732831193 421 89 10 0.112359550561798 0.0237529691211401
GO:CC GO:0031982 vesicle 0.00874098512868588 4055 11 8 0.727272727272727 0.00197287299630086
GO:CC GO:0071944 cell periphery 0.0100537910839177 6169 43 25 0.581395348837209 0.00405252066785541
GO:CC GO:0072562 blood microparticle 0.0100948890596984 140 89 5 0.0561797752808989 0.0357142857142857
GO:CC GO:0009986 cell surface 0.0222542287836367 899 46 8 0.173913043478261 0.00889877641824249
GO:CC GO:0031225 anchored component of membrane 0.0275070272910969 174 59 4 0.0677966101694915 0.0229885057471264
GO:CC GO:0030141 secretory granule 0.0301727660875518 851 7 3 0.428571428571429 0.00352526439482961
GO:CC GO:0035580 specific granule lumen 0.0301727660875518 61 88 3 0.0340909090909091 0.0491803278688525
GO:CC GO:0031093 platelet alpha granule lumen 0.0361678539271212 66 89 3 0.0337078651685393 0.0454545454545455
GO:CC GO:0034774 secretory granule lumen 0.0374766478483717 320 89 6 0.0674157303370786 0.01875
GO:CC GO:0060205 cytoplasmic vesicle lumen 0.038363743023368 324 89 6 0.0674157303370786 0.0185185185185185
GO:CC GO:0031983 vesicle lumen 0.038363743023368 326 89 6 0.0674157303370786 0.0184049079754601
GO:CC GO:0099503 secretory vesicle 0.0393673835933609 1020 7 3 0.428571428571429 0.00294117647058824
GO:MF GO:0070492 oligosaccharide binding 1.34183093298977e-07 15 3 3 1 0.2
GO:MF GO:0042834 peptidoglycan binding 1.34183093298977e-07 18 3 3 1 0.166666666666667
GO:MF GO:0005539 glycosaminoglycan binding 0.000243221765836984 238 3 3 1 0.0126050420168067
GO:MF GO:0030246 carbohydrate binding 0.000281885215467858 275 3 3 1 0.0109090909090909
GO:MF GO:0060089 molecular transducer activity 0.00220172200184767 1458 4 4 1 0.00274348422496571
GO:MF GO:0038023 signaling receptor activity 0.00220172200184767 1458 4 4 1 0.00274348422496571
GO:MF GO:0038024 cargo receptor activity 0.0134795633490857 78 36 3 0.0833333333333333 0.0384615384615385
GO:MF GO:0097367 carbohydrate derivative binding 0.0257190549167166 2285 5 4 0.8 0.00175054704595186
GO:MF GO:0004252 serine-type endopeptidase activity 0.0288607003884992 171 51 4 0.0784313725490196 0.0233918128654971
GO:MF GO:0004896 cytokine receptor activity 0.0311574630717422 99 43 3 0.0697674418604651 0.0303030303030303
GO:MF GO:0008236 serine-type peptidase activity 0.0311574630717422 189 51 4 0.0784313725490196 0.0211640211640212
GO:MF GO:0017171 serine hydrolase activity 0.0311574630717422 193 51 4 0.0784313725490196 0.0207253886010363
GO:MF GO:0050839 cell adhesion molecule binding 0.0334520239880056 546 32 5 0.15625 0.00915750915750916
GO:MF GO:0005102 signaling receptor binding 0.0440299616665606 1672 18 6 0.333333333333333 0.00358851674641148
GO:MF GO:0008233 peptidase activity 0.0440299616665606 646 30 5 0.166666666666667 0.00773993808049536
GO:MF GO:0004175 endopeptidase activity 0.0440299616665606 450 28 4 0.142857142857143 0.00888888888888889
GO:MF GO:0140375 immune receptor activity 0.0440299616665606 133 43 3 0.0697674418604651 0.0225563909774436
REAC REAC:R-HSA-6803157 Antimicrobial peptides 0.0336430042133693 80 67 5 0.0746268656716418 0.0625

pEpi14 transcription factor target enrichment of top program genes

TF enrichment of pEpi14
Possible regulators of activation of pEpi14 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.