TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1790/PPE27:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1787/PPE25	(cc=0.7137)	info on Rv1787/PPE25
Rv1789/PPE26	(cc=0.6094)	info on Rv1789/PPE26
Rv1793/esxN	(cc=0.5777)	info on Rv1793/esxN
Rv1065/-	(cc=0.5621)	info on Rv1065/-
Rv3253c/-	(cc=0.5166)	info on Rv3253c/-
Rv1589/bioB	(cc=0.5016)	info on Rv1589/bioB
Rv1978/-	(cc=0.4969)	info on Rv1978/-
Rv1405c/-	(cc=0.4874)	info on Rv1405c/-
Rv2781c/-	(cc=0.4824)	info on Rv2781c/-
Rv2605c/tesB2	(cc=0.4795)	info on Rv2605c/tesB2

Correlation of Rv1790/PPE27 with Rv1787/PPE25

Normalized LFCs for Rv1790/PPE27:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv1790/PPE27	Rv1787/PPE25
Fe_supp_jason_reseq	-0.36	-0.851
low_pH_jason_reseq	-1.364	-1.655
NO_jason_reseq	0.664	-0.042
B6_jason_reseq	-1.212	-1.404
MHCII_jason_reseq	-1.733	-1.249
Isoniazid02	-0.148	0.308
Rifampicin4	0.349	0.842
Ethambutol3	0.238	0.372
Meropenem3	1.151	0.574
Vancomycin16	-0.586	-0.398
Rv2680_day32	0.027	0.419
H37Rv_KO_MarP	0.01	-0.1
hypoxia_3wks	0.319	0.267
hypoxia_6wks	-0.209	0.0
glycerol	-0.983	0.041
cholesterol	-1.986	-0.952
AJ	0.118	0.492
Bibs02	-0.514	0.221
Bibs02c	-1.102	-0.029
BL6	-0.609	0.067
BL6a	-0.881	0.158
BXD01	-0.438	0.369
BXD010	-0.57	0.332
BXD011	-0.458	0.413
BXD03	-0.157	0.551
BXD04	-0.441	0.157
BXD05	0.143	0.695
BXD06	-0.764	0.237
BXD07	-0.029	0.622
BXD08	-0.338	0.401
BXD09	-0.534	0.435
CAST	-0.444	-0.008
CCcont	-0.515	0.056
DS01	-1.343	-0.476
DS02	-1.081	0.022
DS04	-0.398	0.559
DS0c	-1.226	0.044
GP01	0.544	0.916
GP02	1.099	1.683
GP0c	0.016	0.736
NOD	-0.687	-0.039
NZO	-0.501	0.342
PWK	-0.004	0.337
H37Rv_KO_CtpC	-0.031	0.718
H37Rv_KO_CtpD	0.061	0.635
H37Rv_KO_Rv1272	0.189	0.769
H37Rv_KO_SugABC	-0.115	0.657
H37Rv_KO_MbtN	0.455	0.831
Trans05	0.611	0.971
macrophage_unactivated	0.145	0.41
IL1	0.32	0.501
Rapamycin	-0.288	-0.021
Tcell	0.863	0.632
GMCSF	1.135	1.009
IFNab	-0.65	-0.577
IFNg	0.82	1.013
IFNg_GMCSF1	0.559	0.886
Rv1432_day32	0.372	0.394
Rv1565c_day32	-1.579	-0.581
secA2_input	0.246	0.504
delta_Rv3594	-0.298	-0.171
delta_Rv3717	-0.526	-0.298
delta_Rv3811	-0.251	-0.228
delta_Rv0954	-0.607	-0.238
PonA1	-0.526	-0.602
EccD1_KO	0.257	-0.043
EspI_KO	0.117	0.371
PE35_KO	0.251	0.327
PPE68_KO	0.058	-0.186
glycerol2	0.398	0.017
lignocerate	-0.119	-0.3
oleate	0.431	0.517
phosphatidylcholine	0.601	0.353
acetate	0.076	-0.229
glucAc	0.225	-0.284
Rv0950ko	0.507	0.323
Rv1096ko	-0.621	-0.688
Rv3684ko	-0.377	-0.793
delta_otsA_trehalose	0.056	0.776