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 Rv1302/rfe:

update plot	correlation	link to info on gene
Rv0110/-	(cc=0.4599)	info on Rv0110/-
Rv0877/-	(cc=0.4526)	info on Rv0877/-
Rv0047c/-	(cc=0.444)	info on Rv0047c/-
Rv0158/-	(cc=0.4328)	info on Rv0158/-
Rv2957/-	(cc=0.4311)	info on Rv2957/-
Rv0182c/sigG	(cc=0.4139)	info on Rv0182c/sigG
Rv1072/-	(cc=0.407)	info on Rv1072/-
Rv2617c/-	(cc=0.4012)	info on Rv2617c/-
Rv3853/rraA	(cc=0.3996)	info on Rv3853/rraA
Rv2079/-	(cc=0.3978)	info on Rv2079/-

Correlation of Rv1302/rfe with Rv2617c/-

Normalized LFCs for Rv1302/rfe:
(description and provenance of datasets)

	Rv1302/rfe	Rv2617c/-
Fe_supp_jason_reseq	1.437	0.153
low_pH_jason_reseq	0.465	-1.099
NO_jason_reseq	1.173	0.294
B6_jason_reseq	0.957	0.007
MHCII_jason_reseq	-0.309	0.04
Isoniazid02	0.453	1.15
Rifampicin4	-0.192	-0.119
Ethambutol3	0.732	1.493
Meropenem3	0.502	0.176
Vancomycin16	0.18	0.072
Rv2680_day32	1.779	2.011
H37Rv_KO_MarP	-0.766	0.236
hypoxia_3wks	-0.14	-0.275
hypoxia_6wks	-0.146	-0.217
glycerol	-0.054	-0.064
cholesterol	-1.01	-0.116
AJ	0.674	0.613
Bibs02	-0.968	-0.289
Bibs02c	-0.268	-0.088
BL6	-1.086	0.292
BL6a	0.154	0.595
BXD01	0.737	0.884
BXD010	0.115	0.347
BXD011	0.931	0.563
BXD03	-0.444	0.511
BXD04	0.228	0.452
BXD05	0.201	0.79
BXD06	0.786	0.302
BXD07	0.285	0.762
BXD08	1.099	0.751
BXD09	0.88	0.506
CAST	1.525	0.277
CCcont	-0.791	0.053
DS01	-0.527	0.091
DS02	-0.09	0.117
DS04	-0.672	-0.701
DS0c	-0.671	0.613
GP01	1.155	0.681
GP02	0.603	0.612
GP0c	0.907	0.829
NOD	0.952	0.293
NZO	0.053	0.984
PWK	0.026	0.149
H37Rv_KO_CtpC	1.292	-0.149
H37Rv_KO_CtpD	1.526	0.524
H37Rv_KO_Rv1272	0.598	0.434
H37Rv_KO_SugABC	0.171	-0.091
H37Rv_KO_MbtN	1.816	-0.025
Trans05	0.611	0.431
macrophage_unactivated	-0.069	0.278
IL1	-0.332	-0.166
Rapamycin	-1.295	-0.242
Tcell	0.404	-0.046
GMCSF	-0.615	0.304
IFNab	-0.704	-0.251
IFNg	0.168	-0.38
IFNg_GMCSF1	-0.654	0.189
Rv1432_day32	0.305	0.668
Rv1565c_day32	-0.294	0.472
secA2_input	1.169	-1.119
delta_Rv3594	-0.369	0.236
delta_Rv3717	-0.5	0.088
delta_Rv3811	-0.407	-0.509
delta_Rv0954	-0.934	0.137
PonA1	-0.082	0.0
EccD1_KO	-0.082	0.895
EspI_KO	0.761	0.419
PE35_KO	0.07	-0.009
PPE68_KO	0.586	0.026
glycerol2	0.838	0.818
lignocerate	0.175	0.715
oleate	1.191	1.326
phosphatidylcholine	0.957	0.845
acetate	-0.032	-0.023
glucAc	-0.039	-0.215
Rv0950ko	1.185	0.905
Rv1096ko	0.492	0.296
Rv3684ko	1.844	1.045
delta_otsA_trehalose	-0.662	0.086