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 Rv0072/-:

update plot	correlation	link to info on gene
Rv3156/nuoL	(cc=0.5911)	info on Rv3156/nuoL
Rv0260c/-	(cc=0.5906)	info on Rv0260c/-
Rv1500/-	(cc=0.5792)	info on Rv1500/-
Rv1917c/PPE34	(cc=0.569)	info on Rv1917c/PPE34
Rv3429/PPE59	(cc=0.5667)	info on Rv3429/PPE59
Rv3487c/lipF	(cc=0.5657)	info on Rv3487c/lipF
Rv2430c/PPE41	(cc=0.5657)	info on Rv2430c/PPE41
Rv0059/-	(cc=0.5612)	info on Rv0059/-
Rv3142c/-	(cc=0.5593)	info on Rv3142c/-
Rv2107/PE22	(cc=0.5398)	info on Rv2107/PE22

Correlation of Rv0072/- with Rv2107/PE22

Normalized LFCs for Rv0072/-:
(description and provenance of datasets)

	Rv0072/-	Rv2107/PE22
Fe_supp_jason_reseq	-0.362	-0.93
low_pH_jason_reseq	-0.049	-0.472
NO_jason_reseq	0.0	-0.858
B6_jason_reseq	-0.064	-1.443
MHCII_jason_reseq	-0.69	-1.253
Isoniazid02	-1.484	-0.025
Rifampicin4	0.225	-0.401
Ethambutol3	1.0	0.938
Meropenem3	0.265	-1.12
Vancomycin16	-1.013	-0.671
Rv2680_day32	-0.869	-1.021
H37Rv_KO_MarP	0.49	-0.358
hypoxia_3wks	-0.546	0.275
hypoxia_6wks	-0.194	1.036
glycerol	-0.279	-1.491
cholesterol	0.012	-1.491
AJ	0.24	2.279
Bibs02	0.84	0.568
Bibs02c	0.791	1.285
BL6	0.855	1.493
BL6a	0.816	1.277
BXD01	0.493	0.869
BXD010	0.642	1.557
BXD011	0.508	1.128
BXD03	0.366	0.567
BXD04	0.45	1.035
BXD05	0.87	1.159
BXD06	0.744	1.482
BXD07	0.723	0.903
BXD08	0.582	1.153
BXD09	0.086	1.253
CAST	0.47	0.809
CCcont	0.543	0.081
DS01	1.047	0.76
DS02	-0.112	0.06
DS04	1.737	2.183
DS0c	0.559	-0.061
GP01	0.569	1.842
GP02	0.645	0.492
GP0c	0.418	0.627
NOD	0.111	-0.447
NZO	-0.354	-0.236
PWK	0.539	-0.171
H37Rv_KO_CtpC	0.552	0.812
H37Rv_KO_CtpD	1.424	0.354
H37Rv_KO_Rv1272	1.122	1.809
H37Rv_KO_SugABC	0.979	1.565
H37Rv_KO_MbtN	0.703	0.451
Trans05	1.394	1.754
macrophage_unactivated	0.114	-0.41
IL1	0.119	-0.979
Rapamycin	-0.043	-1.228
Tcell	0.489	-1.235
GMCSF	-0.388	-0.768
IFNab	0.16	-1.563
IFNg	0.246	0.241
IFNg_GMCSF1	-0.145	-0.914
Rv1432_day32	0.263	0.258
Rv1565c_day32	0.896	1.106
secA2_input	-0.762	0.091
delta_Rv3594	-0.174	1.231
delta_Rv3717	-0.366	-0.091
delta_Rv3811	-0.277	0.0
delta_Rv0954	-0.674	0.253
PonA1	0.005	-1.17
EccD1_KO	-0.391	0.118
EspI_KO	-0.094	0.516
PE35_KO	-0.335	0.172
PPE68_KO	-0.259	0.611
glycerol2	1.003	0.083
lignocerate	1.056	-0.203
oleate	1.041	0.567
phosphatidylcholine	0.473	0.482
acetate	0.336	-0.49
glucAc	0.188	-1.046
Rv0950ko	0.078	0.621
Rv1096ko	-0.181	-0.793
Rv3684ko	-0.468	-0.462
delta_otsA_trehalose	-0.703	-0.173