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 Rv3187/-:

update plot	correlation	link to info on gene
Rv3185/-	(cc=0.9611)	info on Rv3185/-
Rv2649/-	(cc=0.9604)	info on Rv2649/-
Rv1756c/-	(cc=0.9599)	info on Rv1756c/-
Rv0796/-	(cc=0.9563)	info on Rv0796/-
Rv2167c/-	(cc=0.956)	info on Rv2167c/-
Rv2279/-	(cc=0.9555)	info on Rv2279/-
Rv3475/-	(cc=0.9544)	info on Rv3475/-
Rv3326/-	(cc=0.9515)	info on Rv3326/-
Rv2355/-	(cc=0.9513)	info on Rv2355/-
Rv1369c/-	(cc=0.9504)	info on Rv1369c/-

Correlation of Rv3187/- with Rv0796/-

Normalized LFCs for Rv3187/-:
(description and provenance of datasets)

	Rv3187/-	Rv0796/-
Fe_supp_jason_reseq	-0.646	-0.455
low_pH_jason_reseq	-0.571	-0.366
NO_jason_reseq	0.165	0.207
B6_jason_reseq	-0.598	-0.312
MHCII_jason_reseq	-0.095	0.066
Isoniazid02	-0.122	-0.063
Rifampicin4	0.59	0.977
Ethambutol3	0.37	0.428
Meropenem3	-0.48	-0.361
Vancomycin16	-0.318	-0.048
Rv2680_day32	0.127	0.211
H37Rv_KO_MarP	-0.147	-0.205
hypoxia_3wks	0.494	0.714
hypoxia_6wks	0.031	0.267
glycerol	-0.772	-0.878
cholesterol	0.125	0.007
AJ	1.301	1.259
Bibs02	1.102	1.07
Bibs02c	1.544	1.676
BL6	0.171	0.132
BL6a	0.954	1.017
BXD01	0.523	0.599
BXD010	0.722	0.851
BXD011	0.739	0.846
BXD03	0.722	0.668
BXD04	0.458	0.374
BXD05	0.933	0.95
BXD06	0.424	0.53
BXD07	0.835	0.738
BXD08	0.411	0.58
BXD09	0.642	0.749
CAST	1.078	1.213
CCcont	-0.034	0.024
DS01	0.739	1.08
DS02	0.788	0.941
DS04	1.003	1.119
DS0c	0.919	1.263
GP01	1.172	1.275
GP02	1.381	1.231
GP0c	0.613	0.611
NOD	1.222	1.383
NZO	1.017	0.877
PWK	1.206	1.178
H37Rv_KO_CtpC	0.725	0.608
H37Rv_KO_CtpD	0.739	0.761
H37Rv_KO_Rv1272	0.516	0.357
H37Rv_KO_SugABC	0.718	0.887
H37Rv_KO_MbtN	0.54	0.523
Trans05	0.823	0.671
macrophage_unactivated	-0.609	-0.644
IL1	-0.38	-0.4
Rapamycin	-0.371	-0.583
Tcell	-0.951	-0.877
GMCSF	-0.069	-0.251
IFNab	-0.883	-0.928
IFNg	-0.211	-0.273
IFNg_GMCSF1	-0.104	-0.217
Rv1432_day32	0.443	0.317
Rv1565c_day32	0.073	0.415
secA2_input	0.202	-0.042
delta_Rv3594	-0.118	0.057
delta_Rv3717	-0.234	-0.122
delta_Rv3811	-0.012	-0.028
delta_Rv0954	0.368	0.895
PonA1	0.047	0.223
EccD1_KO	-0.023	0.0
EspI_KO	0.856	0.781
PE35_KO	0.712	0.779
PPE68_KO	0.579	0.365
glycerol2	-0.961	-0.886
lignocerate	-0.745	-0.547
oleate	-1.15	-0.839
phosphatidylcholine	-0.916	-0.706
acetate	-0.163	0.201
glucAc	0.088	0.106
Rv0950ko	0.229	0.109
Rv1096ko	0.712	0.021
Rv3684ko	-0.364	-0.17
delta_otsA_trehalose	-0.052	0.482