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 Rv2296/-:

update plot	correlation	link to info on gene
Rv1733c/-	(cc=0.5323)	info on Rv1733c/-
Rv3120/-	(cc=0.5317)	info on Rv3120/-
Rv2042c/-	(cc=0.5277)	info on Rv2042c/-
Rv2827c/-	(cc=0.5051)	info on Rv2827c/-
Rv2599/-	(cc=0.4852)	info on Rv2599/-
Rv2980/-	(cc=0.4766)	info on Rv2980/-
Rv3736/-	(cc=0.4619)	info on Rv3736/-
Rv2639c/-	(cc=0.4577)	info on Rv2639c/-
Rv2174/mptA	(cc=0.4525)	info on Rv2174/mptA
Rv1646/PE17	(cc=0.4464)	info on Rv1646/PE17

Correlation of Rv2296/- with Rv1646/PE17

Normalized LFCs for Rv2296/-:
(description and provenance of datasets)

	Rv2296/-	Rv1646/PE17
Fe_supp_jason_reseq	0.044	0.358
low_pH_jason_reseq	-0.146	-0.348
NO_jason_reseq	0.192	0.181
B6_jason_reseq	-0.606	0.787
MHCII_jason_reseq	-0.186	0.025
Isoniazid02	-0.017	0.661
Rifampicin4	0.152	0.439
Ethambutol3	0.058	0.48
Meropenem3	-0.133	-0.279
Vancomycin16	-0.011	-0.167
Rv2680_day32	0.351	0.621
H37Rv_KO_MarP	-0.102	-0.195
hypoxia_3wks	0.195	0.267
hypoxia_6wks	0.2	-0.654
glycerol	0.0	0.329
cholesterol	-0.134	0.325
AJ	0.146	0.948
Bibs02	0.056	0.13
Bibs02c	0.199	0.606
BL6	-0.164	-0.783
BL6a	0.0	0.445
BXD01	0.284	0.031
BXD010	0.005	-0.225
BXD011	0.109	-0.667
BXD03	-0.926	-0.788
BXD04	-0.308	0.394
BXD05	0.659	-0.054
BXD06	0.018	-0.508
BXD07	0.069	-0.498
BXD08	0.245	0.082
BXD09	-0.019	-0.457
CAST	0.077	1.018
CCcont	-0.679	-0.333
DS01	0.332	0.631
DS02	-0.496	0.597
DS04	-0.041	0.396
DS0c	0.707	1.196
GP01	-0.326	0.043
GP02	1.042	0.312
GP0c	0.061	0.025
NOD	0.709	0.765
NZO	-0.007	0.525
PWK	0.246	0.479
H37Rv_KO_CtpC	-0.194	0.071
H37Rv_KO_CtpD	0.131	-0.623
H37Rv_KO_Rv1272	-0.322	-0.306
H37Rv_KO_SugABC	0.325	-0.135
H37Rv_KO_MbtN	-0.014	0.468
Trans05	-0.298	-0.072
macrophage_unactivated	0.0	-0.729
IL1	-0.528	-1.103
Rapamycin	-0.074	-1.264
Tcell	-0.371	-0.026
GMCSF	-0.18	-0.855
IFNab	-0.057	-1.403
IFNg	0.283	-1.213
IFNg_GMCSF1	-0.408	-0.698
Rv1432_day32	0.233	-0.339
Rv1565c_day32	0.287	-0.488
secA2_input	0.477	-0.067
delta_Rv3594	0.902	0.219
delta_Rv3717	0.464	-0.447
delta_Rv3811	0.857	0.089
delta_Rv0954	-0.045	-0.167
PonA1	0.439	0.194
EccD1_KO	1.204	0.49
EspI_KO	0.73	0.351
PE35_KO	1.205	0.397
PPE68_KO	1.353	0.873
glycerol2	0.601	0.573
lignocerate	0.029	0.32
oleate	1.0	0.763
phosphatidylcholine	0.402	0.882
acetate	-0.289	-0.253
glucAc	-0.705	-0.363
Rv0950ko	0.368	0.606
Rv1096ko	-0.299	-0.817
Rv3684ko	-0.373	-0.321
delta_otsA_trehalose	-1.025	-1.123