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 Rv3511/PE_PGRS55:

update plot	correlation	link to info on gene
Rv0834c/PE_PGRS14	(cc=0.7185)	info on Rv0834c/PE_PGRS14
Rv3508/PE_PGRS54	(cc=0.6409)	info on Rv3508/PE_PGRS54
Rv3512/PE_PGRS56	(cc=0.5701)	info on Rv3512/PE_PGRS56
Rv0235c/-	(cc=0.5471)	info on Rv0235c/-
Rv3514/PE_PGRS57	(cc=0.5468)	info on Rv3514/PE_PGRS57
Rv3345c/PE_PGRS50	(cc=0.5418)	info on Rv3345c/PE_PGRS50
Rv1891/-	(cc=0.5372)	info on Rv1891/-
Rv0833/PE_PGRS13	(cc=0.5355)	info on Rv0833/PE_PGRS13
Rv3394c/-	(cc=0.5008)	info on Rv3394c/-
Rv0354c/PPE7	(cc=0.5006)	info on Rv0354c/PPE7

Correlation of Rv3511/PE_PGRS55 with Rv1891/-

Normalized LFCs for Rv3511/PE_PGRS55:
(description and provenance of datasets)

	Rv3511/PE_PGRS55	Rv1891/-
Fe_supp_jason_reseq	-0.718	0.152
low_pH_jason_reseq	-0.269	0.182
NO_jason_reseq	-0.278	-0.58
B6_jason_reseq	-0.682	-1.736
MHCII_jason_reseq	0.111	-2.1
Isoniazid02	-1.059	-0.856
Rifampicin4	0.444	-0.436
Ethambutol3	-0.565	-1.052
Meropenem3	-0.213	-0.55
Vancomycin16	-0.348	0.013
Rv2680_day32	-0.922	0.038
H37Rv_KO_MarP	0.014	0.416
hypoxia_3wks	-0.618	-0.072
hypoxia_6wks	-1.347	-1.194
glycerol	0.686	0.148
cholesterol	0.429	-0.331
AJ	0.844	1.151
Bibs02	-0.334	-2.375
Bibs02c	0.685	-0.534
BL6	-0.228	0.932
BL6a	0.321	1.036
BXD01	0.31	1.005
BXD010	-0.196	0.766
BXD011	-0.297	0.785
BXD03	1.067	1.371
BXD04	0.287	-0.082
BXD05	0.589	0.39
BXD06	0.178	0.93
BXD07	0.41	1.317
BXD08	0.632	1.423
BXD09	0.287	1.202
CAST	0.075	0.389
CCcont	-0.025	1.191
DS01	-0.866	-0.736
DS02	-0.112	0.326
DS04	-0.083	0.103
DS0c	-0.484	-0.553
GP01	0.579	0.477
GP02	1.313	1.328
GP0c	0.699	1.587
NOD	-0.322	0.208
NZO	1.052	1.017
PWK	0.374	0.0
H37Rv_KO_CtpC	0.561	1.865
H37Rv_KO_CtpD	0.302	0.924
H37Rv_KO_Rv1272	0.058	0.869
H37Rv_KO_SugABC	0.649	0.657
H37Rv_KO_MbtN	0.319	1.416
Trans05	1.249	1.462
macrophage_unactivated	0.073	0.615
IL1	-0.59	-0.394
Rapamycin	-0.611	0.246
Tcell	-0.479	-0.355
GMCSF	0.544	0.116
IFNab	-0.683	0.747
IFNg	-0.497	0.158
IFNg_GMCSF1	-0.421	-0.575
Rv1432_day32	1.036	-0.022
Rv1565c_day32	-0.524	0.379
secA2_input	0.446	0.063
delta_Rv3594	-0.135	0.102
delta_Rv3717	-0.53	-0.072
delta_Rv3811	-0.349	-1.029
delta_Rv0954	-0.808	-0.662
PonA1	0.0	-0.19
EccD1_KO	0.444	-0.26
EspI_KO	-0.225	0.334
PE35_KO	-0.63	-0.193
PPE68_KO	-0.733	-0.522
glycerol2	0.248	-0.446
lignocerate	0.342	-0.409
oleate	0.166	-0.489
phosphatidylcholine	0.221	-0.598
acetate	-0.057	-0.218
glucAc	-0.023	-0.234
Rv0950ko	0.609	0.724
Rv1096ko	0.531	0.368
Rv3684ko	-0.193	0.0
delta_otsA_trehalose	-1.443	-0.84