Post by jakec on Jun 21, 2022 14:31:09 GMT -5
Hello,
I am analyzing dog (Canis lupus familiaris) gene lists and I recently noticed that I am getting dramatically different results from the various GO analyses for the same gene lists compared to before. This is despite same genes, gene IDs, and background. Here are some of the results I previously received from June 13...
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0001525~angiogenesis 25 1.7158544955387784 4.5186561184853055E-7 481162, 485122, 489306, 485671, 483808, 478328, 489271, 403727, 607616, 476202, 490138, 403420, 487261, 608972, 487380, 609940, 475923, 481280, 488550, 610031, 474778, 475108, 474578, 609626, 607724 972 119 15113 3.2664609053497946 0.0013542274812795574 0.001355144969933743 0.0013528856418745005
GOTERM_BP_DIRECT GO:0033674~positive regulation of kinase activity 15 1.029512697323267 1.0603910402347932E-5 481105, 479962, 483021, 489557, 484990, 482154, 494006, 487380, 485671, 403811, 608946, 478925, 100856477, 403727, 478987 972 57 15113 4.091672081438163 0.031300952576551966 0.010629763724450365 0.01061204154418286
GOTERM_BP_DIRECT GO:0030335~positive regulation of cell migration 27 1.8531228551818806 1.0633308160503867E-5 479460, 403754, 482252, 489689, 484990, 483386, 486756, 480557, 607976, 403727, 100855988, 442939, 488942, 487731, 486940, 483098, 489775, 483895, 481432, 487380, 475929, 475923, 403811, 100856563, 475882, 479446, 607724 972 160 15113 2.623784722222222 0.03138635398227563 0.010629763724450365 0.01061204154418286
GOTERM_BP_DIRECT GO:0016477~cell migration 28 1.9217570350034316 6.320608753263482E-5 480630, 480034, 482252, 119864507, 476290, 482154, 612913, 490132, 607631, 119868383, 608968, 475431, 403727, 476202, 482986, 482920, 403543, 477351, 487731, 488368, 485536, 484006, 485930, 490660, 483260, 475882, 475108, 100856566 972 187 15113 2.328095772540217 0.17267779041439457 0.04738876412759296 0.04730975651817716
GOTERM_BP_DIRECT GO:0007010~cytoskeleton organization 13 0.8922443376801648 8.696001216834616E-5 482513, 487764, 612904, 119864507, 484006, 477828, 477609, 489694, 477965, 490117, 474976, 100683200, 100856566 972 52 15113 3.887088477366255 0.2295684113627785 0.052158615298574025 0.05207165528640568
GOTERM_BP_DIRECT GO:0007165~signal transduction 48 3.2944406314344548 2.5782050809525914E-4 477220, 486915, 100856417, 403652, 478470, 481748, 479540, 485189, 485166, 483200, 490280, 610879, 610855, 608981, 403809, 608246, 487992, 485396, 611451, 486001, 474762, 489172, 476565, 479215, 476202, 477139, 475272, 478046, 431695, 481633, 403782, 488706, 403543, 479177, 486608, 491738, 486665, 489632, 480203, 483996, 475607, 484073, 475904, 610031, 481917, 476179, 609626, 491038 972 431 15113 1.731603219615594 0.5385139231341072 0.11816850689948359 0.11797149371692359
GOTERM_BP_DIRECT GO:0098609~cell-cell adhesion 12 0.823610158 0.025048878 403572, 609940, 607140, 481280, 403752, 403456, 403401, 477032, 489689, 485158, 111090044, 488008 972 88 15113 2.120230079 1 1 0.998665777
Compared to today.....
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0098609~cell-cell adhesion 6 0.5249343832020997 0.0044330980967838655 403572, 403752, 403456, 403401, 477032, 488008 118 15 1483 5.027118644067796 0.9402049539870175 1.0 1.0
GOTERM_BP_DIRECT GO:0006412~translation 8 0.699912510936133 0.012068427325830957 403681, 607481, 611398, 485132, 403722, 609491, 403506, 403691 118 33 1483 3.046738572162301 0.9995462335256102 1.0 1.0
GOTERM_BP_DIRECT GO:0070830~bicellular tight junction assembly 3 0.26246719160104987 0.0750437830418297 403752, 477032, 403844 118 6 1483 6.283898305084746 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0046777~protein autophosphorylation 3 0.26246719160104987 0.09976310498934589 403811, 491160, 482154 118 7 1483 5.386198547215496 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0031532~actin cytoskeleton reorganization 3 0.26246719160104987 0.09976310498934589 481280, 403754, 403811 118 7 1483 5.386198547215496 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0000187~activation of MAPK activity 3 0.26246719160104987 0.09976310498934589 403811, 483021, 607724 118 7 1483 5.386198547215496 1.0 1.0 1.0
It seems like many of the genes that were considered for the analysis previously are now not ending up in the output. KEGG and other annotation lists do not appear to be impacted. When I make an abbreviated list with only the gene IDs from previous positive hits, again most of the genes end up on the "not in the output" list. Was there an update to the canine annotation the may have lead to this?
Thank you.
I am analyzing dog (Canis lupus familiaris) gene lists and I recently noticed that I am getting dramatically different results from the various GO analyses for the same gene lists compared to before. This is despite same genes, gene IDs, and background. Here are some of the results I previously received from June 13...
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0001525~angiogenesis 25 1.7158544955387784 4.5186561184853055E-7 481162, 485122, 489306, 485671, 483808, 478328, 489271, 403727, 607616, 476202, 490138, 403420, 487261, 608972, 487380, 609940, 475923, 481280, 488550, 610031, 474778, 475108, 474578, 609626, 607724 972 119 15113 3.2664609053497946 0.0013542274812795574 0.001355144969933743 0.0013528856418745005
GOTERM_BP_DIRECT GO:0033674~positive regulation of kinase activity 15 1.029512697323267 1.0603910402347932E-5 481105, 479962, 483021, 489557, 484990, 482154, 494006, 487380, 485671, 403811, 608946, 478925, 100856477, 403727, 478987 972 57 15113 4.091672081438163 0.031300952576551966 0.010629763724450365 0.01061204154418286
GOTERM_BP_DIRECT GO:0030335~positive regulation of cell migration 27 1.8531228551818806 1.0633308160503867E-5 479460, 403754, 482252, 489689, 484990, 483386, 486756, 480557, 607976, 403727, 100855988, 442939, 488942, 487731, 486940, 483098, 489775, 483895, 481432, 487380, 475929, 475923, 403811, 100856563, 475882, 479446, 607724 972 160 15113 2.623784722222222 0.03138635398227563 0.010629763724450365 0.01061204154418286
GOTERM_BP_DIRECT GO:0016477~cell migration 28 1.9217570350034316 6.320608753263482E-5 480630, 480034, 482252, 119864507, 476290, 482154, 612913, 490132, 607631, 119868383, 608968, 475431, 403727, 476202, 482986, 482920, 403543, 477351, 487731, 488368, 485536, 484006, 485930, 490660, 483260, 475882, 475108, 100856566 972 187 15113 2.328095772540217 0.17267779041439457 0.04738876412759296 0.04730975651817716
GOTERM_BP_DIRECT GO:0007010~cytoskeleton organization 13 0.8922443376801648 8.696001216834616E-5 482513, 487764, 612904, 119864507, 484006, 477828, 477609, 489694, 477965, 490117, 474976, 100683200, 100856566 972 52 15113 3.887088477366255 0.2295684113627785 0.052158615298574025 0.05207165528640568
GOTERM_BP_DIRECT GO:0007165~signal transduction 48 3.2944406314344548 2.5782050809525914E-4 477220, 486915, 100856417, 403652, 478470, 481748, 479540, 485189, 485166, 483200, 490280, 610879, 610855, 608981, 403809, 608246, 487992, 485396, 611451, 486001, 474762, 489172, 476565, 479215, 476202, 477139, 475272, 478046, 431695, 481633, 403782, 488706, 403543, 479177, 486608, 491738, 486665, 489632, 480203, 483996, 475607, 484073, 475904, 610031, 481917, 476179, 609626, 491038 972 431 15113 1.731603219615594 0.5385139231341072 0.11816850689948359 0.11797149371692359
GOTERM_BP_DIRECT GO:0098609~cell-cell adhesion 12 0.823610158 0.025048878 403572, 609940, 607140, 481280, 403752, 403456, 403401, 477032, 489689, 485158, 111090044, 488008 972 88 15113 2.120230079 1 1 0.998665777
Compared to today.....
Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0098609~cell-cell adhesion 6 0.5249343832020997 0.0044330980967838655 403572, 403752, 403456, 403401, 477032, 488008 118 15 1483 5.027118644067796 0.9402049539870175 1.0 1.0
GOTERM_BP_DIRECT GO:0006412~translation 8 0.699912510936133 0.012068427325830957 403681, 607481, 611398, 485132, 403722, 609491, 403506, 403691 118 33 1483 3.046738572162301 0.9995462335256102 1.0 1.0
GOTERM_BP_DIRECT GO:0070830~bicellular tight junction assembly 3 0.26246719160104987 0.0750437830418297 403752, 477032, 403844 118 6 1483 6.283898305084746 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0046777~protein autophosphorylation 3 0.26246719160104987 0.09976310498934589 403811, 491160, 482154 118 7 1483 5.386198547215496 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0031532~actin cytoskeleton reorganization 3 0.26246719160104987 0.09976310498934589 481280, 403754, 403811 118 7 1483 5.386198547215496 1.0 1.0 1.0
GOTERM_BP_DIRECT GO:0000187~activation of MAPK activity 3 0.26246719160104987 0.09976310498934589 403811, 483021, 607724 118 7 1483 5.386198547215496 1.0 1.0 1.0
It seems like many of the genes that were considered for the analysis previously are now not ending up in the output. KEGG and other annotation lists do not appear to be impacted. When I make an abbreviated list with only the gene IDs from previous positive hits, again most of the genes end up on the "not in the output" list. Was there an update to the canine annotation the may have lead to this?
Thank you.