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 Rv0112/gca:

update plot	correlation	link to info on gene
Rv2430c/PPE41	(cc=0.6914)	info on Rv2430c/PPE41
Rv1918c/PPE35	(cc=0.6414)	info on Rv1918c/PPE35
Rv2735c/-	(cc=0.6295)	info on Rv2735c/-
Rv0907/-	(cc=0.6282)	info on Rv0907/-
Rv0469/umaA	(cc=0.6168)	info on Rv0469/umaA
Rv3218/-	(cc=0.6008)	info on Rv3218/-
Rv0059/-	(cc=0.5935)	info on Rv0059/-
Rv1505c/-	(cc=0.5928)	info on Rv1505c/-
Rv1059/-	(cc=0.5885)	info on Rv1059/-
Rv3864/espE	(cc=0.587)	info on Rv3864/espE

Correlation of Rv0112/gca with Rv0469/umaA

Normalized LFCs for Rv0112/gca:
(description and provenance of datasets)

	Rv0112/gca	Rv0469/umaA
Fe_supp_jason_reseq	0.415	1.002
low_pH_jason_reseq	1.335	0.125
NO_jason_reseq	0.171	0.039
B6_jason_reseq	0.292	-0.616
MHCII_jason_reseq	-0.342	-0.862
Isoniazid02	0.636	-0.34
Rifampicin4	-0.165	-0.558
Ethambutol3	1.454	0.193
Meropenem3	-0.359	0.291
Vancomycin16	0.157	-0.403
Rv2680_day32	-0.383	-1.846
H37Rv_KO_MarP	-0.223	0.119
hypoxia_3wks	0.53	0.12
hypoxia_6wks	0.142	0.157
glycerol	-0.753	0.565
cholesterol	-0.469	0.048
AJ	1.239	0.397
Bibs02	-0.682	-0.411
Bibs02c	0.887	0.297
BL6	0.839	-0.021
BL6a	1.663	1.129
BXD01	1.652	0.624
BXD010	1.81	1.099
BXD011	2.088	0.879
BXD03	1.673	0.588
BXD04	0.581	1.348
BXD05	0.747	0.997
BXD06	1.26	0.761
BXD07	1.073	0.856
BXD08	0.987	0.705
BXD09	1.384	0.815
CAST	0.569	0.292
CCcont	0.701	0.379
DS01	0.236	-0.482
DS02	0.711	0.744
DS04	0.254	0.663
DS0c	0.815	-0.355
GP01	0.067	1.709
GP02	0.109	0.189
GP0c	1.478	0.803
NOD	1.054	-0.197
NZO	0.548	0.425
PWK	1.088	0.718
H37Rv_KO_CtpC	0.966	0.812
H37Rv_KO_CtpD	1.023	1.551
H37Rv_KO_Rv1272	1.427	2.299
H37Rv_KO_SugABC	0.976	1.213
H37Rv_KO_MbtN	1.612	0.693
Trans05	2.074	1.456
macrophage_unactivated	0.139	0.426
IL1	0.0	-0.258
Rapamycin	0.203	-0.457
Tcell	0.554	0.44
GMCSF	0.655	0.288
IFNab	-0.429	0.127
IFNg	0.345	0.361
IFNg_GMCSF1	0.779	0.465
Rv1432_day32	-0.164	0.162
Rv1565c_day32	0.065	-0.027
secA2_input	-1.342	-1.124
delta_Rv3594	0.035	0.75
delta_Rv3717	0.141	0.367
delta_Rv3811	-0.219	0.568
delta_Rv0954	-0.726	0.18
PonA1	0.382	1.236
EccD1_KO	-0.572	-0.339
EspI_KO	-1.132	-0.756
PE35_KO	-0.755	-1.178
PPE68_KO	-0.691	-0.806
glycerol2	-0.234	-0.02
lignocerate	-0.374	-0.218
oleate	0.474	0.461
phosphatidylcholine	-0.056	0.204
acetate	-0.17	-0.244
glucAc	-0.722	-0.555
Rv0950ko	0.374	0.311
Rv1096ko	-0.48	-0.41
Rv3684ko	-0.599	-0.799
delta_otsA_trehalose	2.09	0.097