pEpi18 program activity among Epithelial cells

Activation of pEpi18
pEpi18 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 pEpi18 by different cell subtypes
pEpi18 gene program activation among cells of different subtypes (Epithelial cells).

pEpi18 top program genes

Top genes of pEpi18 program
Bar plots showing the top genes for each gene program, ranked by (left) unique weights, (right) raw weights.

pEpi18 gene-set enrichment of top program genes (using g-profiler)

GSEA wth gene profiler of pEpi18
pEpi18 gene-set enrichment summary using g-profiler webtool.
Source termID Name Padj Tsize Qsize Overlap Precision Recall
GO:BP GO:0007167 enzyme linked receptor protein signaling pathway 0.0266678380485411 1103 115 19 0.165217391304348 0.0172257479601088
GO:BP GO:0007015 actin filament organization 0.0266678380485411 445 108 11 0.101851851851852 0.0247191011235955
GO:BP GO:0001825 blastocyst formation 0.0266678380485411 38 34 3 0.0882352941176471 0.0789473684210526
GO:BP GO:0048523 negative regulation of cellular process 0.0266678380485411 5139 61 32 0.524590163934426 0.00622689239151586
GO:BP GO:0050789 regulation of biological process 0.0266678380485411 12091 88 75 0.852272727272727 0.00620296087999338
GO:BP GO:0065007 biological regulation 0.0361046357236785 12809 88 77 0.875 0.00601139823561558
GO:BP GO:0050794 regulation of cellular process 0.0361046357236785 11473 88 72 0.818181818181818 0.00627560359103983
GO:BP GO:0001676 long-chain fatty acid metabolic process 0.0361046357236785 112 134 6 0.0447761194029851 0.0535714285714286
GO:BP GO:0030029 actin filament-based process 0.0361046357236785 808 91 13 0.142857142857143 0.0160891089108911
GO:BP GO:0042127 regulation of cell population proliferation 0.0361046357236785 1774 72 18 0.25 0.0101465614430665
GO:BP GO:0002274 myeloid leukocyte activation 0.0361046357236785 667 123 14 0.113821138211382 0.0209895052473763
GO:BP GO:0046456 icosanoid biosynthetic process 0.0361046357236785 56 87 4 0.0459770114942529 0.0714285714285714
GO:BP GO:0030036 actin cytoskeleton organization 0.0385326213479896 709 91 12 0.131868131868132 0.0169252468265162
GO:BP GO:0043299 leukocyte degranulation 0.0417990608989628 535 122 12 0.0983606557377049 0.0224299065420561
GO:BP GO:0030041 actin filament polymerization 0.0417990608989628 196 82 6 0.0731707317073171 0.0306122448979592
GO:BP GO:0070887 cellular response to chemical stimulus 0.0452361604498927 3393 130 41 0.315384615384615 0.0120837017388742
GO:BP GO:0051716 cellular response to stimulus 0.046220279244217 7781 131 76 0.580152671755725 0.00976738208456497
GO:BP GO:0050909 sensory perception of taste 0.046220279244217 67 105 4 0.0380952380952381 0.0597014925373134
GO:BP GO:0050896 response to stimulus 0.046220279244217 9407 131 87 0.66412213740458 0.00924843201870947
GO:BP GO:0048844 artery morphogenesis 0.046220279244217 77 36 3 0.0833333333333333 0.038961038961039
GO:BP GO:0048522 positive regulation of cellular process 0.046220279244217 5757 123 57 0.463414634146341 0.0099009900990099
GO:BP GO:0048519 negative regulation of biological process 0.046220279244217 5757 61 32 0.524590163934426 0.0055584505819003
GO:BP GO:0048518 positive regulation of biological process 0.046220279244217 6363 123 61 0.495934959349593 0.00958667295300959
GO:BP GO:0008154 actin polymerization or depolymerization 0.046220279244217 223 82 6 0.0731707317073171 0.0269058295964126
GO:BP GO:0045321 leukocyte activation 0.046220279244217 1332 130 21 0.161538461538462 0.0157657657657658
GO:BP GO:0043067 regulation of programmed cell death 0.046220279244217 1582 61 14 0.229508196721311 0.00884955752212389
GO:BP GO:0012501 programmed cell death 0.046220279244217 2143 61 17 0.278688524590164 0.00793280447970135
GO:BP GO:0036230 granulocyte activation 0.046220279244217 504 122 11 0.0901639344262295 0.0218253968253968
GO:BP GO:1901570 fatty acid derivative biosynthetic process 0.046220279244217 61 44 3 0.0681818181818182 0.0491803278688525
GO:BP GO:0008284 positive regulation of cell population proliferation 0.0493412206004031 982 56 10 0.178571428571429 0.010183299389002
GO:CC GO:0005737 cytoplasm 0.00544308999490721 11911 63 55 0.873015873015873 0.00461758038787675
GO:CC GO:1903561 extracellular vesicle 0.0264227804084581 2261 39 13 0.333333333333333 0.00574966828836798
GO:CC GO:0070062 extracellular exosome 0.0264227804084581 2176 54 16 0.296296296296296 0.00735294117647059
GO:CC GO:0043230 extracellular organelle 0.0264227804084581 2263 39 13 0.333333333333333 0.00574458683163942
GO:CC GO:0015629 actin cytoskeleton 0.0264227804084581 513 24 5 0.208333333333333 0.00974658869395711
GO:CC GO:0031234 extrinsic component of cytoplasmic side of plasma membrane 0.0276370914494327 102 35 3 0.0857142857142857 0.0294117647058824
GO:CC GO:0005622 intracellular anatomical structure 0.0276370914494327 14790 65 61 0.938461538461538 0.00412440838404327
GO:CC GO:0005884 actin filament 0.0276370914494327 118 108 5 0.0462962962962963 0.0423728813559322
GO:CC GO:0005829 cytosol 0.0276370914494327 5303 89 39 0.438202247191011 0.00735432773901565
GO:CC GO:0031982 vesicle 0.0276370914494327 4055 54 22 0.407407407407407 0.00542540073982737
GO:CC GO:0005856 cytoskeleton 0.0282913003383334 2332 28 10 0.357142857142857 0.00428816466552316
GO:CC GO:0005768 endosome 0.0282913003383334 987 130 16 0.123076923076923 0.0162107396149949
GO:CC GO:0043209 myelin sheath 0.0282913003383334 47 84 3 0.0357142857142857 0.0638297872340425
GO:CC GO:0043005 neuron projection 0.0318168301262472 1380 88 15 0.170454545454545 0.0108695652173913
GO:CC GO:0043228 non-membrane-bounded organelle 0.0318168301262472 5346 17 11 0.647058823529412 0.00205761316872428
GO:CC GO:0043232 intracellular non-membrane-bounded organelle 0.0318168301262472 5338 17 11 0.647058823529412 0.00206069689022106
GO:CC GO:0005886 plasma membrane 0.0390427745615063 5681 123 52 0.422764227642276 0.0091533180778032
GO:CC GO:0045121 membrane raft 0.0417734175982187 335 34 4 0.117647058823529 0.0119402985074627
GO:CC GO:0098857 membrane microdomain 0.0417734175982187 335 34 4 0.117647058823529 0.0119402985074627
GO:CC GO:0030054 cell junction 0.0465135471486625 2105 26 8 0.307692307692308 0.00380047505938242
GO:CC GO:0019898 extrinsic component of membrane 0.0465135471486625 313 43 4 0.0930232558139535 0.012779552715655
GO:CC GO:0044297 cell body 0.0465135471486625 592 105 9 0.0857142857142857 0.0152027027027027
GO:CC GO:0019897 extrinsic component of plasma membrane 0.0465135471486625 176 35 3 0.0857142857142857 0.0170454545454545
GO:CC GO:0097708 intracellular vesicle 0.0465135471486625 2428 130 28 0.215384615384615 0.0115321252059308
GO:CC GO:0098562 cytoplasmic side of membrane 0.0465135471486625 194 35 3 0.0857142857142857 0.0154639175257732
GO:CC GO:0099513 polymeric cytoskeletal fiber 0.0465135471486625 764 41 6 0.146341463414634 0.00785340314136126
GO:CC GO:0016459 myosin complex 0.0465135471486625 57 108 3 0.0277777777777778 0.0526315789473684
GO:CC GO:0009898 cytoplasmic side of plasma membrane 0.0465135471486625 168 35 3 0.0857142857142857 0.0178571428571429
GO:CC GO:0031410 cytoplasmic vesicle 0.0465135471486625 2424 130 28 0.215384615384615 0.0115511551155116
GO:CC GO:0005667 transcription regulator complex 0.0471366685779117 432 121 8 0.0661157024793388 0.0185185185185185
GO:CC GO:0005635 nuclear envelope 0.0471366685779117 467 48 5 0.104166666666667 0.0107066381156317
GO:CC GO:0005615 extracellular space 0.0471366685779117 3594 3 3 1 0.000834724540901503
GO:CC GO:0101002 ficolin-1-rich granule 0.0471366685779117 184 120 5 0.0416666666666667 0.0271739130434783
GO:CC GO:0031965 nuclear membrane 0.0471366685779117 298 48 4 0.0833333333333333 0.0134228187919463
GO:CC GO:0043229 intracellular organelle 0.0492758398960899 12491 62 50 0.806451612903226 0.00400288207509407
GO:CC GO:1904813 ficolin-1-rich granule lumen 0.0492758398960899 124 118 4 0.0338983050847458 0.032258064516129
GO:CC GO:1990904 ribonucleoprotein complex 0.0493930618250972 688 12 3 0.25 0.00436046511627907
GO:MF GO:0140031 phosphorylation-dependent protein binding 0.00100325659228942 6 114 3 0.0263157894736842 0.5
GO:MF GO:0005516 calmodulin binding 0.0196392374908888 204 26 4 0.153846153846154 0.0196078431372549
GO:MF GO:0001784 phosphotyrosine residue binding 0.0196392374908888 44 114 4 0.0350877192982456 0.0909090909090909
GO:MF GO:0048306 calcium-dependent protein binding 0.0248310035753527 82 29 3 0.103448275862069 0.0365853658536585
GO:MF GO:0005515 protein binding 0.0248310035753527 14767 63 60 0.952380952380952 0.00406311369946502
GO:MF GO:0045309 protein phosphorylated amino acid binding 0.0248310035753527 56 114 4 0.0350877192982456 0.0714285714285714
GO:MF GO:0044877 protein-containing complex binding 0.0266468939706612 1287 16 6 0.375 0.00466200466200466
GO:MF GO:0017111 nucleoside-triphosphatase activity 0.0306369701070432 872 17 5 0.294117647058824 0.00573394495412844
GO:MF GO:0004715 non-membrane spanning protein tyrosine kinase activity 0.0306369701070432 46 72 3 0.0416666666666667 0.0652173913043478
GO:MF GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.0306369701070432 930 17 5 0.294117647058824 0.00537634408602151
GO:MF GO:0016817 hydrolase activity, acting on acid anhydrides 0.0306369701070432 930 17 5 0.294117647058824 0.00537634408602151
GO:MF GO:0051213 dioxygenase activity 0.0306369701070432 96 39 3 0.0769230769230769 0.03125
GO:MF GO:0016462 pyrophosphatase activity 0.0306369701070432 928 17 5 0.294117647058824 0.00538793103448276
GO:MF GO:0051219 phosphoprotein binding 0.0377355140189537 88 52 3 0.0576923076923077 0.0340909090909091
GO:MF GO:0003714 transcription corepressor activity 0.0427426038533527 187 101 5 0.0495049504950495 0.0267379679144385
GO:MF GO:0003924 GTPase activity 0.0427426038533527 328 16 3 0.1875 0.00914634146341463
GO:MF GO:0017124 SH3 domain binding 0.0427426038533527 129 85 4 0.0470588235294118 0.0310077519379845
GO:MF GO:0005543 phospholipid binding 0.0427426038533527 454 126 9 0.0714285714285714 0.0198237885462555
GO:MF GO:0004725 protein tyrosine phosphatase activity 0.0429197135179582 103 120 4 0.0333333333333333 0.0388349514563107
GO:MF GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding 0.0436724532872452 281 107 6 0.0560747663551402 0.0213523131672598
GO:MF GO:0016787 hydrolase activity 0.0436724532872452 2615 17 7 0.411764705882353 0.00267686424474187
GO:MF GO:0003779 actin binding 0.0436724532872452 448 15 3 0.2 0.00669642857142857
GO:MF GO:0019899 enzyme binding 0.0445421788692714 2074 61 14 0.229508196721311 0.00675024108003857
GO:MF GO:0008289 lipid binding 0.0445421788692714 776 126 12 0.0952380952380952 0.0154639175257732
GO:MF GO:0004713 protein tyrosine kinase activity 0.0486582316119471 144 98 4 0.0408163265306122 0.0277777777777778
MIRNA MIRNA:hsa-miR-548t-5p hsa-miR-548t-5p 0.0124028338228714 267 82 9 0.109756097560976 0.0337078651685393
MIRNA MIRNA:hsa-miR-548az-5p hsa-miR-548az-5p 0.0124028338228714 267 82 9 0.109756097560976 0.0337078651685393
MIRNA MIRNA:hsa-miR-4639-3p hsa-miR-4639-3p 0.0329550690290119 187 55 6 0.109090909090909 0.0320855614973262
REAC REAC:R-HSA-391160 Signal regulatory protein family interactions 0.0304880360556299 14 52 3 0.0576923076923077 0.214285714285714
REAC REAC:R-HSA-175474 Assembly Of The HIV Virion 0.035795451607267 16 60 3 0.05 0.1875
TF TF:M00342_1 Factor: Oct-1; motif: TATGCAAATN; match class: 1 0.0151485445281423 346 50 8 0.16 0.023121387283237
TF TF:M11491 Factor: LBP9; motif: ACYRGTTNNAACYRGT 0.0218804409576064 5146 55 30 0.545454545454545 0.00582977069568597
TF TF:M08867_1 Factor: AP2; motif: GCCYGSGGSN; match class: 1 0.0244162101725729 5186 122 54 0.442622950819672 0.0104126494408022
TF TF:M10529 Factor: Sp1; motif: RGGGMGGRGSNGGGG 0.0244162101725729 6891 135 71 0.525925925925926 0.0103032941517922
TF TF:M10070_1 Factor: Sox-9; motif: AANGGNNNCWTTGTTY; match class: 1 0.0244162101725729 319 71 8 0.112676056338028 0.0250783699059561
TF TF:M03561 Factor: POU2F1; motif: NNATTTGCATNN 0.0279561062705254 2149 102 26 0.254901960784314 0.0120986505351326
TF TF:M03837 Factor: Oct3; motif: TKWNATGCAWATN 0.0279561062705254 1090 54 12 0.222222222222222 0.0110091743119266
TF TF:M09918_1 Factor: Pet-1; motif: GCNGGAAGYG; match class: 1 0.0279561062705254 7159 128 69 0.5390625 0.00963821762816036
TF TF:M10034 Factor: Oct-2; motif: NYATGCAAATN 0.0324691261329937 6061 50 29 0.58 0.00478468899521531
TF TF:M00161_1 Factor: Oct-1; motif: MKVATTTGCATATT; match class: 1 0.0324691261329937 411 50 7 0.14 0.0170316301703163
TF TF:M04051 Factor: NFATc1; motif: NATGGAAANWNANTTTYCMN 0.0324691261329937 5610 49 27 0.551020408163265 0.00481283422459893
TF TF:M11639_1 Factor: Sox-4; motif: NAACAAAGRN; match class: 1 0.0324691261329937 347 5 3 0.6 0.00864553314121038
TF TF:M00932_1 Factor: Sp1; motif: NNGGGGCGGGGNN; match class: 1 0.0324691261329937 6047 122 58 0.475409836065574 0.00959153299156607
TF TF:M01073 Factor: HIC1; motif: NNNGGKTGCCCSNNNNNN 0.0324691261329937 4088 51 23 0.450980392156863 0.00562622309197652
TF TF:M10072 Factor: sp4; motif: NNGNARGRGGCGGRGCNNRR 0.0324691261329937 10494 132 92 0.696969696969697 0.00876691442729179
TF TF:M10144 Factor: ZNF341; motif: GRGGRRNRGNRGNRGGAASAGC 0.0324691261329937 4766 126 50 0.396825396825397 0.0104909777591272
TF TF:M07059 Factor: POU2F1; motif: ATGCAAATN 0.0335315672122077 1646 102 21 0.205882352941176 0.0127582017010936
TF TF:M08952_1 Factor: NF-KAPPAB1; motif: NGGKRNTTYCCCN; match class: 1 0.0335315672122077 3457 119 38 0.319327731092437 0.0109921897599074
TF TF:M12140 Factor: Egr-1; motif: NNCRCCCMCGCNN 0.0350496288541769 5360 132 56 0.424242424242424 0.0104477611940299
TF TF:M11639 Factor: Sox-4; motif: NAACAAAGRN 0.0350496288541769 3125 12 8 0.666666666666667 0.00256
TF TF:M03893_1 Factor: WT1; motif: GNGGGGGCGGGG; match class: 1 0.035565937014715 3980 132 45 0.340909090909091 0.0113065326633166
TF TF:M00933_1 Factor: Sp1; motif: CCCCGCCCCN; match class: 1 0.035565937014715 5166 122 51 0.418032786885246 0.00987224157955865
TF TF:M11491_1 Factor: LBP9; motif: ACYRGTTNNAACYRGT; match class: 1 0.035565937014715 4149 58 25 0.431034482758621 0.00602554832489757
TF TF:M00342 Factor: Oct-1; motif: TATGCAAATN 0.0372691828337151 2966 106 31 0.292452830188679 0.0104517869184086
TF TF:M11485 Factor: CP2; motif: AACCGGTTNNAACCGGTT 0.0382215698339582 6977 59 35 0.593220338983051 0.0050164827289666
TF TF:M01307 Factor: Oct3; motif: NATGCAANNN 0.0407264456180873 3986 107 38 0.355140186915888 0.0095333667837431
TF TF:M03567_1 Factor: Sp2; motif: NYSGCCCCGCCCCCY; match class: 1 0.0437784239443853 3614 122 39 0.319672131147541 0.0107913669064748
TF TF:M00138_1 Factor: Oct-1; motif: NNNNNNNWATGCAAATNNNWNNA; match class: 1 0.0437784239443853 340 49 6 0.122448979591837 0.0176470588235294
TF TF:M09984 Factor: MAZ; motif: GGGGGAGGGGGNGRGRRRGNRG 0.0437784239443853 9544 122 79 0.647540983606557 0.00827745180217938
TF TF:M04076 Factor: POU3F1; motif: WTATGCWAATNN 0.0468538903032091 610 54 8 0.148148148148148 0.0131147540983607
TF TF:M09826_1 Factor: BTEB3; motif: CCNNSCCNSCCCCKCCCCC; match class: 1 0.0468538903032091 7508 122 66 0.540983606557377 0.00879062333510922
TF TF:M00196_1 Factor: Sp1; motif: NGGGGGCGGGGYN; match class: 1 0.0468538903032091 5919 132 59 0.446969696969697 0.00996789998310525
TF TF:M07058_1 Factor: POU2F1; motif: ATTTGCATN; match class: 1 0.0468538903032091 509 49 7 0.142857142857143 0.0137524557956778

pEpi18 transcription factor target enrichment of top program genes

TF enrichment of pEpi18
Possible regulators of activation of pEpi18 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.