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 Rv3023c/-:

update plot	correlation	link to info on gene
Rv1047/-	(cc=0.9569)	info on Rv1047/-
Rv2666/-	(cc=0.8829)	info on Rv2666/-
Rv3115/-	(cc=0.8696)	info on Rv3115/-
Rv2512c/-	(cc=0.7659)	info on Rv2512c/-
Rv1199c/-	(cc=0.7634)	info on Rv1199c/-
Rv3187/-	(cc=0.689)	info on Rv3187/-
Rv2279/-	(cc=0.6867)	info on Rv2279/-
Rv1369c/-	(cc=0.6681)	info on Rv1369c/-
Rv1756c/-	(cc=0.6668)	info on Rv1756c/-
Rv2355/-	(cc=0.6589)	info on Rv2355/-

Correlation of Rv3023c/- with Rv2666/-

Normalized LFCs for Rv3023c/-:
(description and provenance of datasets)

	Rv3023c/-	Rv2666/-
Fe_supp_jason_reseq	-0.908	-0.736
low_pH_jason_reseq	-0.186	-0.172
NO_jason_reseq	-0.155	-0.134
B6_jason_reseq	-0.704	-0.504
MHCII_jason_reseq	-0.428	-0.307
Isoniazid02	-1.075	-0.626
Rifampicin4	0.257	0.374
Ethambutol3	-0.631	-0.403
Meropenem3	-0.294	0.846
Vancomycin16	-0.82	-0.658
Rv2680_day32	0.098	0.419
H37Rv_KO_MarP	-0.222	0.03
hypoxia_3wks	-0.215	0.255
hypoxia_6wks	-0.785	-0.666
glycerol	0.234	0.367
cholesterol	-0.17	-0.126
AJ	0.931	0.951
Bibs02	1.028	0.486
Bibs02c	1.42	1.985
BL6	0.027	0.662
BL6a	0.809	0.867
BXD01	0.532	0.487
BXD010	0.523	0.372
BXD011	0.257	0.476
BXD03	0.679	0.61
BXD04	0.743	0.489
BXD05	0.952	0.835
BXD06	0.575	0.621
BXD07	0.823	1.017
BXD08	0.328	0.0
BXD09	0.453	0.397
CAST	0.762	1.086
CCcont	0.065	-0.08
DS01	0.366	0.512
DS02	0.985	1.336
DS04	0.528	1.301
DS0c	0.837	0.979
GP01	0.433	0.828
GP02	0.489	0.317
GP0c	0.32	0.578
NOD	0.688	1.287
NZO	0.578	0.498
PWK	0.466	0.705
H37Rv_KO_CtpC	1.194	1.244
H37Rv_KO_CtpD	0.662	1.05
H37Rv_KO_Rv1272	0.747	1.122
H37Rv_KO_SugABC	1.049	0.807
H37Rv_KO_MbtN	0.437	0.558
Trans05	1.11	1.401
macrophage_unactivated	0.268	-0.17
IL1	0.925	0.937
Rapamycin	0.638	-0.132
Tcell	-1.039	-1.183
GMCSF	0.85	0.718
IFNab	0.29	0.46
IFNg	0.032	-0.144
IFNg_GMCSF1	0.688	0.355
Rv1432_day32	-0.402	-0.279
Rv1565c_day32	0.253	-0.079
secA2_input	-0.139	-0.344
delta_Rv3594	0.104	-0.347
delta_Rv3717	-0.37	-0.457
delta_Rv3811	0.0	0.045
delta_Rv0954	-0.056	0.052
PonA1	-0.716	-0.859
EccD1_KO	-0.408	-0.681
EspI_KO	0.083	-0.066
PE35_KO	1.0	0.44
PPE68_KO	0.278	-0.035
glycerol2	-1.386	-1.153
lignocerate	-1.078	-0.774
oleate	-1.171	-1.104
phosphatidylcholine	-1.104	-0.811
acetate	0.685	1.49
glucAc	-0.081	0.446
Rv0950ko	0.0	-0.033
Rv1096ko	-0.489	-0.139
Rv3684ko	-0.301	-0.593
delta_otsA_trehalose	-0.437	-0.722