CLOCK/Salmonella Dataset

1 Network Key
2 Cluster 1
3 Cluster 2
4 Cluster 3
5 Cluster 4

1 Network Key

If node contains this color then it is significant at .05 p-value in that dataset. Can be significant in multiple, or none.

Blue = WT infected vs uninfected day
Green = WT infected vs uninfected night
Brown = CLOCK mutant infected vs uninfected day
Orange = CLOCK mutant infected vs uninfected night

2 Cluster 1

2.1 TFs included in Network

Nfkb2
{'accessions': ['Q9WTK5'], 'comment_similarity': ['Contains 7 ANK repeats.', 'Contains 1 death domain.', 'Contains 1 RHD (Rel-like) domain.'], 'name': 'Nfkb2', 'recommendedName_fullName': ['Nuclear factor NF-kappa-B p100 subunit']}

Hif1a
{'accessions': ['Q61221', 'O08741', 'O08993', 'Q61664', 'Q61665', 'Q8C681', 'Q8CC19', 'Q8CCB6', 'Q8R385', 'Q9CYA8'], 'comment_similarity': ['Contains 1 basic helix-loop-helix (bHLH) domain.', 'Contains 1 PAC (PAS-associated C-terminal) domain.', 'Contains 2 PAS (PER-ARNT-SIM) domains.'], 'name': 'Hif1a', 'recommendedName_fullName': ['Hypoxia-inducible factor 1-alpha'], 'recommendedName_shortName': ['HIF-1-alpha', 'HIF1-alpha']}

Ovol1
{'accessions': ['Q9WTJ2', 'Q545S2'], 'comment_similarity': ['Contains 4 C2H2-type zinc fingers.'], 'name': 'Ovol1', 'recommendedName_fullName': ['Putative transcription factor Ovo-like 1'], 'recommendedName_shortName': ['mOvo1', 'mOvo1a']}

Prdm1
{'accessions': ['Q60636', 'A2VDE8', 'Q3UET9'], 'comment_similarity': ['Contains 4 C2H2-type zinc fingers.', 'Contains 1 SET domain.'], 'name': 'Prdm1', 'recommendedName_fullName': ['PR domain zinc finger protein 1']}

Smad2
{'accessions': ['Q62432', 'Q6GU18', 'Q6VP00', 'Q9D8P6'], 'comment_similarity': ['Belongs to the dwarfin/SMAD family.', 'Contains 1 MH1 (MAD homology 1) domain.', 'Contains 1 MH2 (MAD homology 2) domain.'], 'name': 'Smad2', 'recommendedName_fullName': ['Mothers against decapentaplegic homolog 2'], 'recommendedName_shortName': ['MAD homolog 2', 'Mothers against DPP homolog 2']}

Stat3
{'accessions': ['P42227', 'A2A5D1', 'B7ZC17'], 'comment_similarity': ['Belongs to the transcription factor STAT family.', 'Contains 1 SH2 domain.'], 'name': 'Stat3', 'recommendedName_fullName': ['Signal transducer and activator of transcription 3']}

Arntl/CLOCK
{'accessions': ['Q9WTL8', 'O88295', 'Q921S4', 'Q9R0U2', 'Q9WTL9'], 'comment_similarity': ['Contains 1 basic helix-loop-helix (bHLH) domain.', 'Contains 1 PAC (PAS-associated C-terminal) domain.', 'Contains 2 PAS (PER-ARNT-SIM) domains.'], 'name': 'Arntl', 'recommendedName_fullName': ['Aryl hydrocarbon receptor nuclear translocator-like protein 1']}

Nfkb1
{'accessions': ['P25799', 'Q3TZE8', 'Q3V2V6', 'Q6TDG8', 'Q75ZL1', 'Q80Y21', 'Q8C712'], 'comment_similarity': ['Contains 7 ANK repeats.', 'Contains 1 death domain.', 'Contains 1 RHD (Rel-like) domain.'], 'name': 'Nfkb1', 'recommendedName_fullName': ['Nuclear factor NF-kappa-B p105 subunit']}

Irf8
{'accessions': ['P23611'], 'comment_similarity': ['Belongs to the IRF family.', 'Contains 1 IRF tryptophan pentad repeat DNA-binding domain.'], 'name': 'Irf8', 'recommendedName_fullName': ['Interferon regulatory factor 8'], 'recommendedName_shortName': ['IRF-8']}

Rel
{'accessions': ['P15307'], 'comment_similarity': ['Contains 1 RHD (Rel-like) domain.'], 'name': 'Rel', 'recommendedName_fullName': ['Proto-oncogene c-Rel']}

Rela
{'accessions': ['Q04207', 'Q62025'], 'comment_similarity': ['Contains 1 RHD (Rel-like) domain.'], 'name': 'Rela', 'recommendedName_fullName': ['Transcription factor p65']}

Myc
{'accessions': ['P01108', 'P70247', 'Q3UM70', 'Q61422'], 'comment_similarity': ['Contains 1 basic helix-loop-helix (bHLH) domain.'], 'name': 'Myc', 'recommendedName_fullName': ['Myc proto-oncogene protein']}

Hnf4g
{'accessions': ['Q9WUU6'], 'comment_similarity': ['Belongs to the nuclear hormone receptor family. NR2 subfamily.', 'Contains 1 nuclear receptor DNA-binding domain.'], 'name': 'Hnf4g', 'recommendedName_fullName': ['Hepatocyte nuclear factor 4-gamma'], 'recommendedName_shortName': ['HNF-4-gamma']}

Atf1
{'accessions': ['P81269'], 'comment_similarity': ['Belongs to the bZIP family. ATF subfamily.', 'Contains 1 bZIP domain.', 'Contains 1 KID (kinase-inducible) domain.'], 'name': 'Atf1', 'recommendedName_fullName': ['Cyclic AMP-dependent transcription factor ATF-1'], 'recommendedName_shortName': ['cAMP-dependent transcription factor ATF-1']}

2.2 Networks

2.2.1 TF network (CLOCKTRIMALL)

networks/TF-network.png

2.2.2 Fully-connected TF network (CLOCKTRIMTFALL)

2.2.3 Full network (CLOCKTRIM)

2.2.4 Proteins significant in WT infected vs uninfected day (CLOCKTRIM0)

2.2.5 Proteins significant in WT infected vs uninfected night (CLOCKTRIM1)

2.2.6 Proteins significant in CLOCK mutant infected vs uninfected day (CLOCKTRIM2)

2.2.7 Proteins significant in CLOCK mutant infected vs uninfected night (CLOCKTRIM3)

2.2.8 Difference between CLOCK mutant and WT day (CLOCKTRIM0REMOVED)

2.2.9 Difference between CLOCK mutant and WT night (CLOCKTRIM1REMOVED)

2.3 GO analysis (Top 20 enriched annotations)


	GO Term	Count	Percentage	p-value	Fold Enrichment	Benjamini p-value
1	immune response	53	15.8682634730539	1.45855715729538e-24	5.62136255776196	2.5568506967388e-21
2	response to wounding	39	11.6766467065868	6.00863372959416e-18	5.61463807424987	5.26656746398928e-15
3	inflammatory response	32	9.5808383233533	1.20226439707048e-17	7.10483660130719	7.02523162688182e-15
4	defense response	42	12.5748502994012	1.65261964360520e-16	4.68336397058824	4.86277684785819e-14
5	mmu04621:NOD-like receptor signaling pathway	13	3.89221556886228	1.07871580920171e-08	9.04608294930875	1.26209670292532e-06
6	inflammatory response	13	3.89221556886228	1.21498784480603e-08	9.35744234800839	3.85150407078427e-06
7	cytokine	18	5.38922155688623	1.81339374759809e-08	5.70962583946274	2.87422498335133e-06
8	PIRSF005552:guanine nucleotide-binding protein 1	6	1.79640718562874	1.88446452613451e-07	36.1065088757396	3.65579470036348e-05
9	IPR003191:Guanylate-binding protein, C-terminal	6	1.79640718562874	2.01971601551270e-07	37.4746835443038	0.000150861420868398
10	IPR001811:Small chemokine, interleukin-8-like	9	2.69461077844311	2.20869685477391e-07	13.6731953472460	8.24914340129546e-05
11	cytokine activity	17	5.08982035928144	3.94942817405200e-07	4.88318201469952	0.000178893128349955
12	chemokine activity	9	2.69461077844311	5.04559487901997e-07	12.2457505631784	0.000114276222805798
13	chemokine receptor binding	9	2.69461077844311	6.24279723051955e-07	11.9317569589943	9.42618246763116e-05
14	regulation of cytokine production	15	4.49101796407186	7.1297835304467e-07	5.39092255607279	0.000249939059709492
15	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	12	3.59281437125748	8.30188111897995e-07	7.13655462184874	0.000242523980352738
16	adaptive immune response	12	3.59281437125748	8.30188111897995e-07	7.13655462184874	0.000242523980352738
17	SM00199:SCY	9	2.69461077844311	9.92421443649605e-07	11.1052702702703	0.000168697498120540
18	immune effector process	14	4.19161676646707	1.35897526105141e-06	5.55065359477124	0.000340268560009682
19	IPR015894:Guanylate-binding protein, N-terminal	6	1.79640718562874	1.94578279769702e-06	25.944011684518	0.000484383036624569
20	extracellular region part	34	10.1796407185629	2.10414239539143e-06	2.47419512535792	0.000506970297911691