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 Rv1711/-:

update plot	correlation	link to info on gene
Rv0811c/-	(cc=0.6035)	info on Rv0811c/-
Rv2548A/-	(cc=0.5225)	info on Rv2548A/-
Rv3741c/-	(cc=0.5046)	info on Rv3741c/-
Rv0589/mce2A	(cc=0.4985)	info on Rv0589/mce2A
Rv2581c/-	(cc=0.4905)	info on Rv2581c/-
Rv3905c/esxF	(cc=0.4859)	info on Rv3905c/esxF
Rv2195/qcrA	(cc=0.4838)	info on Rv2195/qcrA
Rv2880c/-	(cc=0.4759)	info on Rv2880c/-
Rv3748/-	(cc=0.4688)	info on Rv3748/-
Rv0990c/-	(cc=0.4576)	info on Rv0990c/-

Correlation of Rv1711/- with Rv2880c/-

Normalized LFCs for Rv1711/-:
(description and provenance of datasets)

	Rv1711/-	Rv2880c/-
Fe_supp_jason_reseq	0.218	-0.338
low_pH_jason_reseq	0.0	-0.813
NO_jason_reseq	0.0	0.512
B6_jason_reseq	0.0	0.677
MHCII_jason_reseq	0.0	0.254
Isoniazid02	0.0	0.058
Rifampicin4	0.374	0.791
Ethambutol3	0.461	0.495
Meropenem3	0.0	-0.01
Vancomycin16	0.0	0.615
Rv2680_day32	0.0	-0.55
H37Rv_KO_MarP	0.195	0.065
hypoxia_3wks	0.0	-0.299
hypoxia_6wks	0.0	-1.002
glycerol	0.0	-0.101
cholesterol	0.0	-0.136
AJ	0.0	0.168
Bibs02	0.0	0.87
Bibs02c	0.0	0.915
BL6	0.0	0.319
BL6a	0.0	0.178
BXD01	0.0	-0.144
BXD010	0.0	0.043
BXD011	0.0	-0.47
BXD03	0.0	0.121
BXD04	0.0	-0.023
BXD05	0.0	0.514
BXD06	0.0	-0.332
BXD07	0.0	0.328
BXD08	0.0	0.133
BXD09	0.0	0.187
CAST	0.0	0.11
CCcont	0.0	-0.302
DS01	0.0	0.392
DS02	0.0	0.469
DS04	0.0	0.937
DS0c	0.0	0.104
GP01	0.0	0.351
GP02	0.0	-0.802
GP0c	0.0	-0.251
NOD	0.0	-0.138
NZO	0.0	0.279
PWK	0.0	0.418
H37Rv_KO_CtpC	0.0	-0.062
H37Rv_KO_CtpD	0.0	0.341
H37Rv_KO_Rv1272	0.0	-0.253
H37Rv_KO_SugABC	0.0	0.362
H37Rv_KO_MbtN	0.103	-0.839
Trans05	0.0	0.25
macrophage_unactivated	0.0	-0.17
IL1	0.0	0.578
Rapamycin	0.0	0.16
Tcell	0.0	-0.381
GMCSF	0.0	0.285
IFNab	0.0	0.048
IFNg	0.0	0.289
IFNg_GMCSF1	0.0	0.867
Rv1432_day32	0.0	0.997
Rv1565c_day32	0.0	0.27
secA2_input	-0.593	0.088
delta_Rv3594	-0.635	-1.169
delta_Rv3717	-1.114	-1.277
delta_Rv3811	-0.501	-1.097
delta_Rv0954	-1.632	-1.151
PonA1	-0.898	-0.733
EccD1_KO	0.414	0.115
EspI_KO	1.791	0.753
PE35_KO	0.0	0.907
PPE68_KO	0.0	0.653
glycerol2	0.0	0.179
lignocerate	0.0	-0.018
oleate	0.0	0.252
phosphatidylcholine	0.0	0.081
acetate	0.0	-0.434
glucAc	0.0	-0.54
Rv0950ko	0.416	0.757
Rv1096ko	0.793	0.072
Rv3684ko	0.452	0.0
delta_otsA_trehalose	-0.122	0.753