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 Rv1429/-:

update plot	correlation	link to info on gene
Rv1719/-	(cc=0.5422)	info on Rv1719/-
Rv3059/cyp136	(cc=0.5362)	info on Rv3059/cyp136
Rv3058c/-	(cc=0.5355)	info on Rv3058c/-
Rv1087A/-	(cc=0.5315)	info on Rv1087A/-
Rv1033c/trcR	(cc=0.5261)	info on Rv1033c/trcR
Rv2517c/-	(cc=0.522)	info on Rv2517c/-
Rv0461/-	(cc=0.5174)	info on Rv0461/-
Rv1148c/-	(cc=0.5128)	info on Rv1148c/-
Rv2599/-	(cc=0.5029)	info on Rv2599/-
Rv3060c/-	(cc=0.4961)	info on Rv3060c/-

Correlation of Rv1429/- with Rv0461/-

Normalized LFCs for Rv1429/-:
(description and provenance of datasets)

	Rv1429/-	Rv0461/-
Fe_supp_jason_reseq	0.548	0.341
low_pH_jason_reseq	-0.415	0.027
NO_jason_reseq	0.142	0.15
B6_jason_reseq	0.463	0.173
MHCII_jason_reseq	0.589	0.809
Isoniazid02	-0.314	-0.893
Rifampicin4	0.049	0.942
Ethambutol3	-0.251	0.61
Meropenem3	-0.722	-0.132
Vancomycin16	-0.199	-0.817
Rv2680_day32	-0.481	0.367
H37Rv_KO_MarP	0.728	1.28
hypoxia_3wks	-0.439	-0.096
hypoxia_6wks	-0.407	-0.328
glycerol	-0.59	0.255
cholesterol	-0.744	0.336
AJ	0.094	0.077
Bibs02	-0.019	-0.519
Bibs02c	-0.182	0.047
BL6	-0.621	-0.569
BL6a	-0.276	0.07
BXD01	-0.636	-0.041
BXD010	-0.523	-0.247
BXD011	0.197	-0.224
BXD03	-0.279	-0.152
BXD04	0.727	0.138
BXD05	-0.007	-0.264
BXD06	-0.708	-0.579
BXD07	-0.081	-0.047
BXD08	0.169	0.559
BXD09	-0.373	-0.175
CAST	0.239	-0.309
CCcont	-0.899	-0.248
DS01	-0.286	-0.214
DS02	-0.547	-0.03
DS04	0.53	0.306
DS0c	0.121	-0.093
GP01	-0.977	-0.795
GP02	-0.177	0.389
GP0c	-0.869	-0.365
NOD	0.034	-0.05
NZO	0.698	-0.056
PWK	-0.628	-0.438
H37Rv_KO_CtpC	0.424	0.248
H37Rv_KO_CtpD	0.246	-0.111
H37Rv_KO_Rv1272	-1.513	-0.71
H37Rv_KO_SugABC	0.079	-0.066
H37Rv_KO_MbtN	-0.785	-0.487
Trans05	-0.363	-0.301
macrophage_unactivated	-0.227	0.698
IL1	-0.166	-0.133
Rapamycin	0.233	0.249
Tcell	-0.209	0.156
GMCSF	-0.042	0.573
IFNab	-0.638	0.221
IFNg	-0.444	0.174
IFNg_GMCSF1	-0.305	-0.214
Rv1432_day32	0.274	0.305
Rv1565c_day32	0.006	0.938
secA2_input	-0.016	0.066
delta_Rv3594	0.044	0.278
delta_Rv3717	-0.486	0.576
delta_Rv3811	0.128	0.247
delta_Rv0954	0.556	1.28
PonA1	0.763	1.09
EccD1_KO	0.385	0.148
EspI_KO	1.252	0.359
PE35_KO	0.866	-0.099
PPE68_KO	0.688	0.154
glycerol2	1.389	0.633
lignocerate	-0.117	0.017
oleate	0.447	0.645
phosphatidylcholine	0.969	0.426
acetate	-0.143	0.175
glucAc	-0.379	0.216
Rv0950ko	0.431	0.051
Rv1096ko	0.347	0.271
Rv3684ko	0.098	0.95
delta_otsA_trehalose	0.051	-0.165