Summer 2021 and 2022 analyses and results streamlined. Details in post. Also - day 1 of Quadra Writing Retreat progress and goals for the rest of the retreat.

Summer 2021 and 2022 Results

Overall step-wise results from each year generally:

  1. Count matrices - number of total genes.
  2. DEG lists - annotated. Numbers higher in control, lower in control. Number annotated, etc.
  3. DAVID: biological processes enrichment and Kegg pathways. Background is uniprot accession IDs from genome BLAST, and gene lists are uniprot accession IDs from DEG lists.
  4. REVIGO: DAVID output - list of GO IDs associated with terms with p-values of <0.05. Too few with Bonferroni significant values, so to create a figure and to have a larger-view of processes to talk about, use the terms with p-values <0.05.
  5. DAVID output: significantly enriched terms –> Bonferroni value <0.05 - talk about the process and genes associated with the significantly enriched.
  6. Genes of interest –> Bonferroni significant genes - talk about them. And, talk about any in the list from REVIGO that are related to immune response.
  7. Can make heatmaps/other figures

Summer 2021

DEG list:
paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2021_exposedVcontrol_annotated.tab

DAVID output:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID_2021_DEGlist.txt

1 significant process with Bonferroni <0.05 (actual value: 0.0002):

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR  
GOTERM_BP_DIRECT GO:0002181~cytoplasmic translation 34 0.74626866 2.76E-08 Q9IA76, P62914, P18101, P49180, P63221, G1SQH0, G1SKF7, Q8JGR4, O09167, Q8CBC7, A0A1D8PF57, O61231, Q6DD06, Q6P799, P47955, P41116, P62907, P55039, P51410, P27085, Q9VXX8, P62861, Q02543, P36241, P61314, Q90YV0, C0HKA1, P27659, P05388, P24049 4235 40 10742 2.15600945 2.00E-04 2.00E-04 2.00E-04  

Found the GO ID term in the list of annotated DEGs from that comparison to get the list of genes (30 genes) related to the Cytoplasmic Translation GO ID:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2021-Bonferroni_genes_from_1_significant.txt

Summer 2022

Comparison A: Control v Exposed:

DEG List: paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_annotated.tab

DAVID Output:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID-2022-controlVexposed.txt

Bonferroni significant processes:

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR  
GOTERM_BP_DIRECT GO:0006511~ubiquitin-dependent protein catabolic process 94 2.14758967 4.19E-08 Q9H0E2, P46471, Q3U1J4, Q9UBF6, Q8BZQ7, Q8CJB9, P53804, Q7TPD1, Q6GPF3, Q8C7R4, P15374, Q9BXM7, Q8BZZ3, Q5E964, Q92890, Q08CZ0, Q6P073, Q9JLV2, Q9Z2U1, Q8BW70, Q6TEM9, Q71U00, Q9H3F6, Q9VBP9, Q9Y5A7, Q15386, Q5PQN1, O43242, Q5RKH6, P60901, Q8QG64, Q810L3, O08759, Q6J1I7, F6UA42, Q9R049, Q3T0J1, F6P3G4, Q96AB6, Q29504, Q9C5D2, Q9P2G1, Q5U2S1, Q9N1T2, Q5SPX3, Q4KLT0, B4F6W9, P46379, Q6ZT12, P49407, Q15751, Q9HAU4, Q5RFS2, Q3URF8, Q6NRG0, Q3ULA2, A9JRZ0, Q9R1P4, Q9ES00, P18101, O95376, A0AVT1, Q9PTW9, Q708Y0, Q923V4, P60670, Q7Z6Z7, P25789, P25788, P25867, Q5ND34, Q91YT2, Q5F3N6, Q8BM54, Q6NW85, P25787, Q4G0X4, Q8TDB6, O88196, Q5ZHY5, Q5R4I2, O95260, Q9CPX9, Q9M622, Q9WVS6, P0C2W1, Q6I6G8, Q80Z37, Q9NV58, Q5XIU5, Q9UMX0, P22682, O95628 4107 156 10742 1.57602717 2.97E-04 2.29E-04 2.29E-04  
GOTERM_BP_DIRECT GO:0016567~protein ubiquitination 167 3.81539867 6.47E-08 Q6INH1, Q91ZT9, Q8WXK3, Q5F4A1, Q91ZT8, Q9R1R2, P53804, Q8CJB9, E1C760, Q5REG4, Q9UPN9, P15374, Q9BXM7, Q9QZN1, Q08CZ0, Q6PFK1, Q9JLV2, P23787, Q5SSH7, Q6TEM9, Q71U00, Q9NXK8, Q58WW2, Q5PQN1, Q8BI21, Q8IWR1, Q5PQN5, Q8CF97, A0JM49, P51593, Q9P1Y6, Q5ZKD9, Q9Y4L5, F6UA42, Q810L3, Q8K0G5, Q8LEV3, Q9Y4D8, Q922Y2, Q3V0Q1, Q3SZD5, Q9N1T2, Q5RCM6, Q4KLT0, B4F6W9, Q5XI67, Q5FVN8, A7E305, Q6ZT12, P49407, Q9HAU4, Q3URF8, Q0IJ33, Q6NRG0, O15541, Q9Z255, A9JRZ0, Q9ES00, P18101, Q5R792, A0AVT1, D3Z902, Q7L622, Q708Y0, Q6DG60, Q5M8S7, Q9NR09, P61963, O35709, Q5ZM55, P79781, Q6NW85, Q93008, Q924T7, P0CG73, Q8HXD5, Q9Y575, Q6PJ21, Q9UPQ7, Q9CPX9, E7FDW2, Q56A24, Q7ZX22, P0C2W1, Q6I6G8, Q96EH8, Q08BU1, P56273, P60882, P22682, O95628, A9JTG5, Q6TDP4, O54928, Q32L65, E9Q4F2, O94822, E1BNS0, Q3U1J4, Q9UBF6, A0A0G2JZ79, Q969H0, Q7TPD1, Q6GPF3, Q8C7R4, P63245, Q8BZZ3, Q8TEJ3, P0CG50, Q13042, B5DF45, Q8K430, Q9H3F6, Q6GPV5, Q9Y5A7, Q5RKH6, A2A6Q5, Q8VBV4, Q8QG64, O08759, Q7L273, F1LZF0, A5HK05, Q8N5D0, Q9UHC7, Q5T447, Q5BJN8, A6H7H7, Q5FWL3, Q9SAL0, O35717, Q9UJX3, Q15751, Q8WV16, Q9D787, Q3ULA2, Q8N806, O70277, Q3TQF0, Q8VHQ4, Q8BGZ4, Q80T85, A0A1D5NVS8, O95376, Q7Z6M2, Q9W3M3, Q6PCX9, Q8VHQ2, Q923V4, Q03601, P62976, P25867, Q8BM54, Q5RB36, Q4G0X4, Q28DS3, O88196, Q28DT9, Q149N8, Q9WVS6, Q5ZIJ9, Q15370, Q93034, Q8BK06, Q9R1A8 4107 314 10742 1.3910645 4.58E-04 2.29E-04 2.29E-04  
GOTERM_BP_DIRECT GO:0002181~cytoplasmic translation 32 0.73109436 4.64E-07 Q9IA76, P18101, P63221, G1SQH0, G1SKF7, Q8JGR4, O09167, Q8CBC7, A0A1D8PF57, O61231, Q6DD06, Q6P799, P47955, P41116, P62907, P51410, D2XV59, P27085, Q9VXX8, Q498T4, P62861, P38983, Q02543, P36241, P61314, Q90YV0, P27659, P05388, P24049 4107 40 10742 2.09242756 0.00328165 9.83E-04 9.82E-04  
GOTERM_BP_DIRECT GO:0006508~proteolysis 194 4.43225954 5.55E-07 P32822, B2RYG6, Q07590, G5ECS8, P59509, Q6P1B1, P48052, Q9Y3Q0, Q8R4K8, Q8C1A5, O15484, Q70CQ4, P62083, G3UZ78, O15519, Q9QX15, P21128, P17945, P25723, Q8BW70, Q5T2D3, A6QR55, Q6ICB0, P07478, P29787, Q86UV5, Q6TH47, Q8CF97, P19221, P12821, Q04592, Q8TE57, P15145, P87362, Q9WVM6, Q62381, B2GUZ1, Q8NHM4, Q8CHN8, Q9CUS9, Q8NFA0, Q5XJY4, A0A2S3R7M0, B6MUN4, O00602, Q08CH3, Q19AZ8, P10619, Q54P70, O43895, Q9CXY9, Q6PZ02, Q9WTR0, Q99PW6, O05218, O43897, A0A0R4IB93, O02467, O57382, Q8NF86, P16444, Q9UDY8, P48147, B5DEQ3, Q93008, O35548, Q9DEX3, P80646, P23004, P45436, Q6GQ29, Q9R0S2, P07858, Q61824, O77656, P17538, Q60692, Q9W436, Q3T0P5, Q00493, Q4WUD3, D3ZPG5, Q3UR85, P39675, P15088, P14272, B1AQJ2, P20825, Q9UQC9, Q92542, Q9NQH7, Q8BHG1, P29119, P80912, Q9ULZ9, Q8BM88, Q9UKP5, Q9VT65, Q9UKP4, Q8IYS1, P56399, Q3UVK0, P20918, P50579, Q5PQY6, Q1JP61, Q3SYW2, O76031, P55866, Q9P2N4, P70505, P21328, Q8I7P9, P70627, Q95M12, Q5G267, Q07943, P0C872, Q4R684, A0A386CAB9, P20231, Q9UI42, P04323, Q9Y5R2, P55115, Q9CZR2, O75976, P21580, P55112, Q96LD8, Q7M760, P70059, Q9D7Z6, P13676, Q5G271, P90850, F8VPZ3, B0BM95, Q5ZIM5, Q8N7X0, P00730, Q8N531, Q09PK2, Q3ULA2, Q9VAC5, P04813, P16519, P58873, P0CT40, A8K7I4, Q86V25, Q96DT6, A3KG59, Q7L266, Q80V42, Q4R7U8, P69527, Q99542, O57579, P00767, Q14790, P54281, Q60928, P98064, Q9NQC7, Q15485, Q9NVE5, Q10751, O15072, Q1JPJ2, Q9CXT6, A3KQS4, F1NV61, Q9JLG8, P70195, Q2T9J0, Q6P8K8, E1C1R4, P53634, P15684, Q3UTY6, Q6Q473, P10394, Q96KP4, Q9JJ22, P52948, Q99497, P08594, P47245, Q5I0D7, Q9I9L7 4107 383 10742 1.32483991 0.00392559 9.83E-04 9.82E-04  

Genes from DEG lists that have the associated GO IDs:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2022-Bonferroni-controlvExposed-genelist.txt

Breakdown of the number of genes for each enriched GO term:

GO ID Term Number of Genes associated with it
GO:0006511 Catabolic Process 79
GO:0016567 Protein Ubiquitination 158
GO:0002181 Cytoplasmic Translation 28
GO:0006508 Proteolysis 190

Cytoplasmic translation was the GO term significantly enriched in the 2021 dataset and 30 genes are associated with it from that dataset - are they the same genes in the 2022 dataset?

28 genes from 2022 that ate associated with the Cytoplasmic Translation GO ID: paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2022-Bonferroni_Cytoplasmic_Translation_genes.tab

Comparison B: Control V Exposed Taking Age Into Account

DEG List:
paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_withAge_annotated.tab

DAVID OUTPUT:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID-2022-controlVexposed-withage.txt

Terms with Bonferroni <0.05:

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0002181~cytoplasmic translation 34 0.77237619 1.40E-08 Q9IA76, P62914, P18101, P49180, P63221, G1SQH0, G1SKF7, Q8JGR4, O09167, Q8CBC7, A0A1D8PF57, O61231, Q6DD06, Q6P799, P47955, P41116, P62907, P51410, D2XV59, P27085, Q9VXX8, Q498T4, P62861, P38983, Q02543, P36241, P61314, Q90YV0, P27659, P05388, P24049 4137 40 10742 2.20708243 9.96E-05 9.96E-05 9.96E-05
GOTERM_BP_DIRECT GO:0006511~ubiquitin-dependent protein catabolic process 93 2.11267606 1.51E-07 Q9H0E2, P46471, Q3U1J4, Q9UBF6, Q8BZQ7, Q8CJB9, P53804, Q7TPD1, Q6GPF3, Q8C7R4, P15374, Q9D4H8, Q9BXM7, Q8BZZ3, Q5E964, Q92890, Q08CZ0, Q6P073, Q9JLV2, Q9Z2U1, Q8BW70, Q6TEM9, Q71U00, Q9H3F6, Q9VBP9, Q9Y5A7, Q15386, Q5PQN1, O43242, Q5RKH6, P60901, Q8QG64, Q810L3, O08759, Q6J1I7, F6UA42, Q9R049, Q3T0J1, F6P3G4, Q29504, Q9P2G1, Q5U2S1, Q9N1T2, Q5SPX3, Q4KLT0, B4F6W9, P46379, Q6ZT12, P49407, Q9HAU4, Q5RFS2, Q3URF8, Q6NRG0, Q3ULA2, A9JRZ0, Q9R1P4, Q9ES00, P18101, O95376, A0AVT1, Q9PTW9, E1B7X3, Q708Y0, Q923V4, P60670, Q7Z6Z7, P25789, P25788, P25867, Q5ND34, Q91YT2, Q5F3N6, Q8BM54, Q6NW85, P25787, Q4G0X4, Q8TDB6, O88196, Q5ZHY5, Q5R4I2, O95260, Q9CPX9, Q9M622, Q9WVS6, P0C2W1, Q6I6G8, Q80Z37, Q9NV58, Q5XIU5, Q9UMX0, P22682, O95628 4137 156 10742 1.54795374 0.00106954 4.98E-04 4.98E-04
GOTERM_BP_DIRECT GO:0016567~protein ubiquitination 166 3.77101318 2.10E-07 Q6INH1, Q91ZT9, Q8WXK3, Q5F4A1, Q91ZT8, Q9R1R2, P53804, Q8CJB9, E1C760, Q5REG4, Q9UPN9, Q9D4H8, P15374, Q9BXM7, Q9QZN1, Q5XH39, Q08CZ0, Q6PFK1, Q9JLV2, P23787, Q8WWI1, Q5SSH7, Q6TEM9, Q71U00, Q9NXK8, Q58WW2, Q5PQN1, Q8BI21, Q5PQN5, Q8CF97, A0JM49, P51593, Q9P1Y6, Q5ZKD9, Q9Y4L5, F6UA42, Q810L3, Q8K0G5, Q8LEV3, Q9Y4D8, Q922Y2, Q3V0Q1, Q3SZD5, Q9N1T2, Q5RCM6, Q4KLT0, B4F6W9, Q5XI67, Q5FVN8, A7E305, Q6ZT12, P49407, Q9HAU4, Q3URF8, Q0IJ33, Q6NRG0, O15541, Q9Z255, A9JRZ0, Q9ES00, P18101, Q5R792, Q5XGG5, A0AVT1, D3Z902, Q7L622, Q708Y0, Q6DG60, Q5M8S7, Q9NR09, P61963, O35709, Q5ZM55, P79781, Q6NW85, Q93008, Q924T7, P0CG73, Q8HXD5, Q6PJ21, Q9UPQ7, Q9CPX9, E7FDW2, Q56A24, Q7ZX22, P0C2W1, Q6I6G8, Q5XGI3, Q96EH8, P56273, P60882, P22682, O95628, Q3TUL7, A9JTG5, Q6TDP4, O54928, E9Q4F2, O94822, E1BNS0, Q3U1J4, Q9UBF6, A0A0G2JZ79, Q969H0, Q7TPD1, Q6GPF3, Q8C7R4, P63245, Q8BZZ3, Q8TEJ3, P0CG50, B5DF45, Q8K430, Q9H3F6, Q6GPV5, Q9Y5A7, Q5RKH6, A2A6Q5, Q8VBV4, P0CE12, Q8QG64, O08759, Q7L273, F1LZF0, A5HK05, Q8N5D0, Q9UHC7, Q5T447, Q5BJN8, A6H7H7, Q5FWL3, Q9SAL0, O35717, Q9UJX3, Q8WV16, Q9D787, Q3ULA2, Q8N806, O70277, Q3TQF0, Q8VHQ4, Q8BGZ4, Q80T85, Q5XGC0, O95376, Q9W3M3, Q6PCX9, Q8VHQ2, Q923V4, Q03601, P62976, P25867, Q8BM54, Q5RB36, Q4G0X4, Q28DS3, O88196, Q5R4Q7, Q149N8, Q9WVS6, Q5ZIJ9, Q93034, Q8BK06, Q9R1A8 4137 314 10742 1.37270769 0.00149374 4.98E-04 4.98E-04
GOTERM_BP_DIRECT GO:0006508~proteolysis 193 4.38437074 1.66E-06 P32822, B2RYG6, Q07590, G5ECS8, P59509, Q6P1B1, P48052, Q9Y3Q0, Q8R4K8, Q8C1A5, O15484, Q70CQ4, P62083, Q9UBB5, G3UZ78, O15519, Q9QX15, P21128, P25723, Q8BW70, Q5T2D3, A6QR55, Q6ICB0, P07478, Q1EHB3, P29787, Q86UV5, Q6TH47, Q8CF97, P19221, P12821, Q04592, Q8TE57, P15145, P87362, Q9WVM6, Q62381, B2GUZ1, A2BGT0, Q8NHM4, Q8CHN8, Q9CUS9, Q8NFA0, Q5XJY4, B6MUN4, O00602, Q08CH3, Q19AZ8, P10619, Q54P70, O43895, Q9CXY9, Q6PZ02, Q9WTR0, Q99PW6, O05218, A0A0R4IB93, O02467, O57382, Q8NF86, P16444, Q9UDY8, P48147, B5DEQ3, Q93008, Q9DEX3, P80646, P23004, P45436, O75636, Q6GQ29, Q9R0S2, P07858, Q61824, O77656, P17538, Q60692, Q9W436, Q3T0P5, Q00493, Q4WUD3, D3ZPG5, Q3UR85, P39675, P15088, P14272, B1AQJ2, P20825, Q9UQC9, Q92542, Q9NQH7, Q8BHG1, P80912, Q9ULZ9, Q8BM88, Q9UKP5, Q9VT65, Q9UKP4, Q8IYS1, P56399, Q3UVK0, P78509, P20918, P50579, Q5PQY6, Q1JP61, Q3SYW2, O76031, P55866, Q9P2N4, P70505, P21328, Q8I7P9, P70627, Q95M12, Q5G267, Q07943, P0C872, Q4R684, A0A386CAB9, P20231, Q9UI42, P04323, Q9Y5R2, P55115, Q9CZR2, O75976, P21580, P55112, Q96LD8, Q7M760, P70059, Q9D7Z6, P13676, Q5G271, P90850, F8VPZ3, B0BM95, Q5ZIM5, Q8N7X0, P00730, Q5JVF3, Q8N531, Q3ULA2, Q9VAC5, P04813, P58873, P0CT40, A8K7I4, Q96DT6, A3KG59, O57460, Q7L266, Q80V42, Q4R7U8, P69527, Q99542, O57579, P00767, Q14790, P54281, Q60928, P98064, Q9NQC7, Q15485, Q9NVE5, Q10751, O15072, Q1JPJ2, Q9CXT6, A3KQS4, F1NV61, Q9JLG8, P70195, P79729, Q2T9J0, Q6P8K8, E1C1R4, P53634, P15684, Q6Q473, P10394, Q96KP4, Q9JJ22, P52948, Q99497, P08594, P47245, Q5I0D7, Q9I9L7 4137 383 10742 1.30845311 0.01172974 0.00294977 0.00294811

Genes associated with those 4 Terms:
List:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2022-Bonferroni-ageintoaccount.txt

Table:

GO ID Term Number of Genes Associated With It
GO:0002181 cytoplasmic translation 31
GO:0006511 ubiquitin-dependent protein catabolic process 79
GO:0016567 protein ubiquitination 159
GO:0006508 proteolysis 190

Comparison C: Age Contrast

DEG list:
paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_withAgeContrast_annotated.tab

DAVID Output:
aper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID-2022-controlVexposed-agecontrast.txt

There are no significantly enriched processes from this group using the corrected Bonferroni p-value. There’s only the 4 Terms that have p-value <0.05:

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GOTERM_BP_DIRECT GO:0051301~cell division 6 11.7647059 0.01007779 P50748, P49454, Q7ZW63, Q8NG31, Q2YDW7, Q15431 46 317 10742 4.41996983 0.92670483 1 1
GOTERM_BP_DIRECT GO:0007155~cell adhesion 5 9.80392157 0.01513702 Q28062, Q8AVH7, Q29116, P22105, Q9Z0G4 46 229 10742 5.09872793 0.98045841 1 1
GOTERM_BP_DIRECT GO:0006826~iron ion transport 2 3.92156863 0.04514821 B3EWZ9 46 11 10742 42.458498 0.99999334 1 1
GOTERM_BP_DIRECT GO:0006825~copper ion transport 2 3.92156863 0.04915234 B3EWZ9 46 12 10742 38.9202899 0.99999775 1 1

Number of genes for each of those terms:

GO ID Term Number of Genes Associated With It
GO:0051301 Cell Division 6
GO:0007155 Cell Adhesion 5
GO:0006826 Iron Ion Transport 1
GO:0006825 Copper Ion Transport 1

Goals for Writing Retreat

Today - Day 1, Monday

Get the results solid, and if time, add to methods section.

Tomorrow - Day 2, Tuesday

Finish methods

Outline overall story of paper

Draft Introduction

Collect papers for Discussion

Day 3, Wednesday

Discussion