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 Rv3819/-

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

	Rv1366/-	Rv3819/-
Fe_supp_jason_reseq	-0.884	-0.451
low_pH_jason_reseq	-0.172	-0.833
NO_jason_reseq	-0.294	-0.452
B6_jason_reseq	-0.871	-0.8
MHCII_jason_reseq	-0.267	-0.487
Isoniazid02	0.148	-0.799
Rifampicin4	-0.376	-0.255
Ethambutol3	0.269	-0.342
Meropenem3	0.237	-0.285
Vancomycin16	0.172	-0.249
Rv2680_day32	-0.969	0.188
H37Rv_KO_MarP	0.518	1.153
hypoxia_3wks	-0.235	-1.348
hypoxia_6wks	-0.048	-0.942
glycerol	-0.78	-0.705
cholesterol	-0.44	-1.165
AJ	0.134	-1.706
Bibs02	-0.823	-0.816
Bibs02c	0.656	-0.321
BL6	0.376	1.018
BL6a	0.397	-0.603
BXD01	0.834	0.406
BXD010	1.115	0.566
BXD011	0.35	-0.777
BXD03	-0.278	-0.581
BXD04	0.315	0.28
BXD05	0.231	-0.295
BXD06	0.323	-0.446
BXD07	0.476	0.602
BXD08	0.506	0.382
BXD09	-0.012	-0.58
CAST	-0.142	0.756
CCcont	0.646	1.057
DS01	0.301	0.736
DS02	-0.254	-0.148
DS04	0.263	0.843
DS0c	0.525	-1.501
GP01	1.227	-2.323
GP02	1.296	-0.576
GP0c	0.54	-2.26
NOD	0.148	2.603
NZO	0.839	0.47
PWK	0.406	1.017
H37Rv_KO_CtpC	0.467	-0.401
H37Rv_KO_CtpD	-0.907	0.763
H37Rv_KO_Rv1272	0.341	-0.833
H37Rv_KO_SugABC	0.902	-0.316
H37Rv_KO_MbtN	0.392	-0.854
Trans05	0.557	-0.605
macrophage_unactivated	0.107	0.956
IL1	-0.739	-1.922
Rapamycin	-0.681	-1.703
Tcell	0.694	0.476
GMCSF	-1.117	-1.584
IFNab	-0.593	-1.542
IFNg	-1.384	-1.732
IFNg_GMCSF1	-1.628	-2.19
Rv1432_day32	-0.55	0.374
Rv1565c_day32	0.175	0.556
secA2_input	-0.188	-1.446
delta_Rv3594	-0.249	-0.304
delta_Rv3717	0.371	-1.016
delta_Rv3811	-0.665	0.586
delta_Rv0954	0.813	0.129
PonA1	0.726	-0.527
EccD1_KO	-0.276	0.724
EspI_KO	0.262	0.248
PE35_KO	0.379	-0.362
PPE68_KO	0.534	0.624
glycerol2	1.188	1.651
lignocerate	1.47	2.557
oleate	0.387	-0.556
phosphatidylcholine	1.27	2.018
acetate	1.549	4.972
glucAc	1.226	2.696
Rv0950ko	0.856	0.148
Rv1096ko	0.32	1.215
Rv3684ko	0.534	0.514
delta_otsA_trehalose	1.077	1.218