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 Rv1366/-:

update plot	correlation	link to info on gene
Rv3749c/-	(cc=0.6056)	info on Rv3749c/-
Rv2078/-	(cc=0.5622)	info on Rv2078/-
Rv1913/-	(cc=0.5434)	info on Rv1913/-
Rv1013/pks16	(cc=0.5409)	info on Rv1013/pks16
Rv2287/yjcE	(cc=0.5232)	info on Rv2287/yjcE
Rv1751/-	(cc=0.5193)	info on Rv1751/-
Rv3697c/vapC48	(cc=0.5103)	info on Rv3697c/vapC48
Rv3819/-	(cc=0.4989)	info on Rv3819/-
Rv0226c/-	(cc=0.4983)	info on Rv0226c/-
Rv0235c/-	(cc=0.4943)	info on Rv0235c/-

Correlation of Rv1366/- with Rv1013/pks16

Normalized LFCs for Rv1366/-:
(description and provenance of datasets)

	Rv1366/-	Rv1013/pks16
Fe_supp_jason_reseq	-0.884	0.48
low_pH_jason_reseq	-0.172	-0.495
NO_jason_reseq	-0.294	1.533
B6_jason_reseq	-0.871	-1.271
MHCII_jason_reseq	-0.267	-3.023
Isoniazid02	0.148	-1.756
Rifampicin4	-0.376	0.019
Ethambutol3	0.269	2.037
Meropenem3	0.237	1.0
Vancomycin16	0.172	-0.236
Rv2680_day32	-0.969	-0.362
H37Rv_KO_MarP	0.518	0.968
hypoxia_3wks	-0.235	-3.334
hypoxia_6wks	-0.048	-3.909
glycerol	-0.78	-0.856
cholesterol	-0.44	-1.194
AJ	0.134	0.435
Bibs02	-0.823	-0.029
Bibs02c	0.656	-1.15
BL6	0.376	1.133
BL6a	0.397	0.319
BXD01	0.834	0.994
BXD010	1.115	2.464
BXD011	0.35	1.442
BXD03	-0.278	2.47
BXD04	0.315	1.886
BXD05	0.231	1.862
BXD06	0.323	1.863
BXD07	0.476	1.419
BXD08	0.506	1.095
BXD09	-0.012	2.209
CAST	-0.142	0.0
CCcont	0.646	2.434
DS01	0.301	-0.636
DS02	-0.254	-0.106
DS04	0.263	0.561
DS0c	0.525	0.919
GP01	1.227	2.567
GP02	1.296	2.671
GP0c	0.54	1.142
NOD	0.148	-0.185
NZO	0.839	-0.342
PWK	0.406	1.903
H37Rv_KO_CtpC	0.467	1.227
H37Rv_KO_CtpD	-0.907	0.133
H37Rv_KO_Rv1272	0.341	0.656
H37Rv_KO_SugABC	0.902	-0.099
H37Rv_KO_MbtN	0.392	1.591
Trans05	0.557	0.998
macrophage_unactivated	0.107	-0.552
IL1	-0.739	-0.917
Rapamycin	-0.681	-0.853
Tcell	0.694	0.984
GMCSF	-1.117	-1.941
IFNab	-0.593	-2.065
IFNg	-1.384	-2.539
IFNg_GMCSF1	-1.628	-2.212
Rv1432_day32	-0.55	0.463
Rv1565c_day32	0.175	1.501
secA2_input	-0.188	-2.481
delta_Rv3594	-0.249	-1.239
delta_Rv3717	0.371	0.375
delta_Rv3811	-0.665	-2.174
delta_Rv0954	0.813	0.823
PonA1	0.726	0.768
EccD1_KO	-0.276	-0.191
EspI_KO	0.262	0.128
PE35_KO	0.379	-1.068
PPE68_KO	0.534	-0.218
glycerol2	1.188	-0.073
lignocerate	1.47	4.396
oleate	0.387	6.0
phosphatidylcholine	1.27	2.531
acetate	1.549	1.438
glucAc	1.226	0.923
Rv0950ko	0.856	-0.956
Rv1096ko	0.32	-0.323
Rv3684ko	0.534	1.166
delta_otsA_trehalose	1.077	-0.506