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 Rv3258c/-:

update plot	correlation	link to info on gene
Rv3789/-	(cc=0.7401)	info on Rv3789/-
Rv3671c/-	(cc=0.6645)	info on Rv3671c/-
Rv2553c/-	(cc=0.6559)	info on Rv2553c/-
Rv3101c/ftsX	(cc=0.6426)	info on Rv3101c/ftsX
Rv1080c/greA	(cc=0.626)	info on Rv1080c/greA
Rv3670/ephE	(cc=0.6211)	info on Rv3670/ephE
Rv1836c/-	(cc=0.6134)	info on Rv1836c/-
Rv0955/-	(cc=0.6074)	info on Rv0955/-
Rv3102c/ftsE	(cc=0.6071)	info on Rv3102c/ftsE
Rv0541c/-	(cc=0.5632)	info on Rv0541c/-

Correlation of Rv3258c/- with Rv1080c/greA

Normalized LFCs for Rv3258c/-:
(description and provenance of datasets)

	Rv3258c/-	Rv1080c/greA
Fe_supp_jason_reseq	0.974	1.121
low_pH_jason_reseq	-0.979	-0.231
NO_jason_reseq	-1.536	0.633
B6_jason_reseq	-0.649	0.267
MHCII_jason_reseq	-0.572	-0.135
Isoniazid02	0.0	-0.851
Rifampicin4	0.0	-0.271
Ethambutol3	0.0	0.505
Meropenem3	0.0	-0.12
Vancomycin16	0.0	-0.546
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-3.852	-2.138
hypoxia_3wks	0.0	-0.55
hypoxia_6wks	0.0	0.503
glycerol	0.0	-0.385
cholesterol	0.0	0.233
AJ	0.232	0.193
Bibs02	0.0	-0.167
Bibs02c	0.0	-0.399
BL6	0.0	-0.114
BL6a	0.0	0.319
BXD01	0.0	-0.119
BXD010	0.0	0.299
BXD011	0.0	0.383
BXD03	0.0	-0.123
BXD04	0.0	0.199
BXD05	0.369	0.57
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.111
BXD09	0.0	0.117
CAST	0.0	-0.21
CCcont	0.525	1.481
DS01	0.0	-0.216
DS02	0.0	-0.414
DS04	2.159	0.312
DS0c	0.0	0.349
GP01	0.0	0.672
GP02	0.0	-0.159
GP0c	0.0	0.551
NOD	0.0	0.361
NZO	0.548	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.261
H37Rv_KO_CtpD	0.348	0.381
H37Rv_KO_Rv1272	0.0	-0.129
H37Rv_KO_SugABC	1.267	0.083
H37Rv_KO_MbtN	0.85	2.002
Trans05	0.0	0.889
macrophage_unactivated	0.0	0.436
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	1.068
Rv1565c_day32	0.0	0.218
secA2_input	1.415	-0.348
delta_Rv3594	2.041	3.356
delta_Rv3717	0.793	3.97
delta_Rv3811	1.737	3.554
delta_Rv0954	-2.153	-2.225
PonA1	-0.63	-1.428
EccD1_KO	-0.97	-3.029
EspI_KO	-1.338	-1.825
PE35_KO	-2.202	-1.747
PPE68_KO	-3.033	-0.755
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	-2.735	-3.35
Rv1096ko	1.143	-1.888
Rv3684ko	0.992	-0.655
delta_otsA_trehalose	0.0	0.906