pEpi29 program activity among Epithelial cells

Activation of pEpi29
pEpi29 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 pEpi29 by different cell subtypes
pEpi29 gene program activation among cells of different subtypes (Epithelial cells).

pEpi29 top program genes

Top genes of pEpi29 program
Bar plots showing the top genes for each gene program, ranked by (left) unique weights, (right) raw weights.

pEpi29 gene-set enrichment of top program genes (using g-profiler)

GSEA wth gene profiler of pEpi29
pEpi29 gene-set enrichment summary using g-profiler webtool.
Source termID Name Padj Tsize Qsize Overlap Precision Recall
GO:BP GO:0002576 platelet degranulation 0.0122893023232514 126 36 5 0.138888888888889 0.0396825396825397
GO:CC GO:0009986 cell surface 0.00535085338799293 899 68 13 0.191176470588235 0.014460511679644
GO:CC GO:0012505 endomembrane system 0.0137169785708958 4640 51 24 0.470588235294118 0.00517241379310345
GO:CC GO:0030667 secretory granule membrane 0.0137169785708958 303 36 5 0.138888888888889 0.0165016501650165
GO:CC GO:0031225 anchored component of membrane 0.0137169785708958 174 61 5 0.0819672131147541 0.028735632183908
GO:CC GO:1903561 extracellular vesicle 0.0137169785708958 2261 22 9 0.409090909090909 0.00398053958425475
GO:CC GO:0070062 extracellular exosome 0.0137169785708958 2176 22 9 0.409090909090909 0.00413602941176471
GO:CC GO:0031091 platelet alpha granule 0.0137169785708958 90 32 3 0.09375 0.0333333333333333
GO:CC GO:0099503 secretory vesicle 0.0137169785708958 1020 36 8 0.222222222222222 0.00784313725490196
GO:CC GO:0005615 extracellular space 0.0137169785708958 3594 23 12 0.521739130434783 0.00333889816360601
GO:CC GO:0005576 extracellular region 0.0137169785708958 4567 28 16 0.571428571428571 0.00350339391285308
GO:CC GO:0043230 extracellular organelle 0.0137169785708958 2263 22 9 0.409090909090909 0.00397702165267344
GO:CC GO:0048770 pigment granule 0.0176945148578276 105 36 3 0.0833333333333333 0.0285714285714286
GO:CC GO:0042470 melanosome 0.0176945148578276 105 36 3 0.0833333333333333 0.0285714285714286
GO:CC GO:0030054 cell junction 0.0176945148578276 2105 80 19 0.2375 0.00902612826603325
GO:CC GO:0030141 secretory granule 0.0176945148578276 851 36 7 0.194444444444444 0.0082256169212691
GO:CC GO:0101002 ficolin-1-rich granule 0.0262055506964259 184 27 3 0.111111111111111 0.016304347826087
GO:CC GO:0031982 vesicle 0.0309043300682132 4055 22 11 0.5 0.00271270036991369
GO:CC GO:0030659 cytoplasmic vesicle membrane 0.0343116401079905 779 36 6 0.166666666666667 0.00770218228498074
GO:CC GO:0031902 late endosome membrane 0.0355602185737752 140 41 3 0.0731707317073171 0.0214285714285714
GO:CC GO:0012506 vesicle membrane 0.035723404942421 800 36 6 0.166666666666667 0.0075
GO:CC GO:0005886 plasma membrane 0.035723404942421 5681 81 36 0.444444444444444 0.00633691251540222
GO:CC GO:0097708 intracellular vesicle 0.035723404942421 2428 41 12 0.292682926829268 0.00494233937397035
GO:CC GO:0071944 cell periphery 0.035723404942421 6169 103 47 0.456310679611651 0.00761873885556816
GO:CC GO:0031410 cytoplasmic vesicle 0.035723404942421 2424 41 12 0.292682926829268 0.00495049504950495
GO:CC GO:0098793 presynapse 0.037671539658215 521 75 7 0.0933333333333333 0.0134357005758157
GO:CC GO:0005783 endoplasmic reticulum 0.0435731811285269 1982 22 7 0.318181818181818 0.00353178607467205
GO:CC GO:0098857 membrane microdomain 0.0442262822922274 335 94 6 0.0638297872340425 0.017910447761194
GO:CC GO:0045121 membrane raft 0.0442262822922274 335 94 6 0.0638297872340425 0.017910447761194
GO:CC GO:0016324 apical plasma membrane 0.0442262822922274 361 39 4 0.102564102564103 0.0110803324099723
GO:MF GO:0098631 cell adhesion mediator activity 0.0223572018202296 58 87 4 0.0459770114942529 0.0689655172413793
GO:MF GO:0042277 peptide binding 0.0368315537459582 314 21 4 0.19047619047619 0.0127388535031847
GO:MF GO:0004857 enzyme inhibitor activity 0.0368315537459582 385 32 5 0.15625 0.012987012987013
GO:MF GO:0098632 cell-cell adhesion mediator activity 0.0420218462197648 49 66 3 0.0454545454545455 0.0612244897959184
GO:MF GO:0033218 amide binding 0.0420218462197648 389 21 4 0.19047619047619 0.0102827763496144
GO:MF GO:0048306 calcium-dependent protein binding 0.0420218462197648 82 97 4 0.0412371134020619 0.0487804878048781
REAC REAC:R-HSA-114608 Platelet degranulation 0.00977244367755954 125 36 5 0.138888888888889 0.04
REAC REAC:R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 0.00977244367755954 130 36 5 0.138888888888889 0.0384615384615385
TF TF:M04823_1 Factor: E2F-4; motif: NNTTCCCGCCNN; match class: 1 0.0127533592419798 7850 104 63 0.605769230769231 0.00802547770700637
TF TF:M01104_1 Factor: MOVO-B; motif: GNGGGGG; match class: 1 0.0127533592419798 5626 98 48 0.489795918367347 0.00853181656594383
TF TF:M07208 Factor: EGR1; motif: NCNCCGCCCCCGCN 0.0127533592419798 6183 85 46 0.541176470588235 0.00743975416464499
TF TF:M11213_1 Factor: AP-4; motif: AHCATRTGKT; match class: 1 0.0127533592419798 3121 12 9 0.75 0.00288369112463954
TF TF:M04148_1 Factor: TFAP2A; motif: NGCCCYNNGGGCN; match class: 1 0.0127533592419798 9613 104 73 0.701923076923077 0.0075938832830542
TF TF:M11211 Factor: AP-4; motif: ANCATATGNT 0.0127533592419798 3216 12 9 0.75 0.00279850746268657
TF TF:M04148 Factor: TFAP2A; motif: NGCCCYNNGGGCN 0.0127533592419798 10040 104 75 0.721153846153846 0.00747011952191235
TF TF:M11362 Factor: c-MAF; motif: NTGCTKAYGTMAGCAN 0.0185498805085356 472 51 8 0.156862745098039 0.0169491525423729
TF TF:M03876_1 Factor: Kaiso; motif: GCMGGGRGCRGS; match class: 1 0.0185498805085356 9106 97 65 0.670103092783505 0.00713815066988799
TF TF:M11533_1 Factor: E2F-1; motif: NTTTTGGCGCCAWWWN; match class: 1 0.0230926733926054 8705 98 63 0.642857142857143 0.00723721998851235
TF TF:M07354_1 Factor: Egr-1; motif: GCGGGGGCGG; match class: 1 0.0230926733926054 3561 97 34 0.350515463917526 0.0095478798090424
TF TF:M11209 Factor: AP-4; motif: ANCATATGNT 0.0230926733926054 3732 12 9 0.75 0.00241157556270096
TF TF:M11209_1 Factor: AP-4; motif: ANCATATGNT; match class: 1 0.0230926733926054 2803 12 8 0.666666666666667 0.00285408490902604
TF TF:M09761 Factor: EGR1; motif: NGNGKGGGYGGNGS 0.0233557660355639 5162 87 40 0.459770114942529 0.00774893452150329
TF TF:M02036_1 Factor: WT1; motif: CGCCCCCNCN; match class: 1 0.0267316706950927 5290 97 44 0.45360824742268 0.00831758034026465
TF TF:M07039_1 Factor: ETF; motif: CCCCGCCCCYN; match class: 1 0.0267316706950927 13611 100 86 0.86 0.00631841892586878
TF TF:M01873_1 Factor: Egr-1; motif: GCGGGGGCGG; match class: 1 0.030507044247584 2672 84 25 0.297619047619048 0.0093562874251497
TF TF:M03896 Factor: EGR1; motif: NACGCCCACGCANW 0.0308509280073524 6129 97 48 0.494845360824742 0.00783162016642193
TF TF:M07084_1 Factor: E2F-4; motif: NGGCGGGAARN; match class: 1 0.0308509280073524 5437 99 45 0.454545454545455 0.00827662313775979
TF TF:M00915 Factor: AP-2; motif: SNNNCCNCAGGCN 0.0308509280073524 9612 99 67 0.676767676767677 0.00697045359966708
TF TF:M10912_1 Factor: pitx2; motif: YTAATCCC; match class: 1 0.0308509280073524 101 94 5 0.0531914893617021 0.0495049504950495
TF TF:M04429_1 Factor: PITX3; motif: NNTAATCCN; match class: 1 0.0308509280073524 101 94 5 0.0531914893617021 0.0495049504950495
TF TF:M08925 Factor: JUNB:C-FOS; motif: NATGAGTCATNN 0.0308509280073524 3490 49 20 0.408163265306122 0.00573065902578797
TF TF:M00333_1 Factor: ZF5; motif: NRNGNGCGCGCWN; match class: 1 0.0308509280073524 12401 98 79 0.806122448979592 0.00637045399564551
TF TF:M11213 Factor: AP-4; motif: AHCATRTGKT 0.0308509280073524 4234 12 9 0.75 0.00212564950401512
TF TF:M09826 Factor: BTEB3; motif: CCNNSCCNSCCCCKCCCCC 0.0329410057177717 11467 97 74 0.762886597938144 0.00645330077614023
TF TF:M04403 Factor: MNX1; motif: NNYAATTAAN 0.0337099495992816 2650 45 16 0.355555555555556 0.0060377358490566
TF TF:M11207 Factor: AP-4; motif: ANCATATGNT 0.0359918117668234 3309 12 8 0.666666666666667 0.0024176488365065
TF TF:M11211_1 Factor: AP-4; motif: ANCATATGNT; match class: 1 0.0370936974276323 2391 12 7 0.583333333333333 0.00292764533667921
TF TF:M03852_1 Factor: SREBP-2; motif: NTCACCYNNNN; match class: 1 0.037369430408858 2246 38 13 0.342105263157895 0.00578806767586821
TF TF:M08934 Factor: JUND; motif: NATGAGTCAT 0.0389890264486551 4329 36 18 0.5 0.00415800415800416
TF TF:M09970 Factor: KLF3; motif: NNNNNNGGGCGGGGCNNGN 0.0410831243029677 7728 104 59 0.567307692307692 0.00763457556935818
TF TF:M09624 Factor: GATA-6; motif: NNNAGATAAGAWAN 0.0468538780650619 3203 22 11 0.5 0.00343428036216047
TF TF:M09734_1 Factor: ZNF692; motif: SYNGGSCCCASCCNC; match class: 1 0.0483519136245819 6255 103 50 0.485436893203884 0.00799360511590727

pEpi29 transcription factor target enrichment of top program genes

TF enrichment of pEpi29
Possible regulators of activation of pEpi29 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.