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 Rv3142c/-:

update plot	correlation	link to info on gene
Rv2106/-	(cc=0.7082)	info on Rv2106/-
Rv2479c/-	(cc=0.7074)	info on Rv2479c/-
Rv2279/-	(cc=0.7018)	info on Rv2279/-
Rv2355/-	(cc=0.7014)	info on Rv2355/-
Rv1764/-	(cc=0.689)	info on Rv1764/-
Rv3185/-	(cc=0.6857)	info on Rv3185/-
Rv2814c/-	(cc=0.6843)	info on Rv2814c/-
Rv3187/-	(cc=0.6772)	info on Rv3187/-
Rv2167c/-	(cc=0.6751)	info on Rv2167c/-
Rv0823c/-	(cc=0.6728)	info on Rv0823c/-

Correlation of Rv3142c/- with Rv2355/-

Normalized LFCs for Rv3142c/-:
(description and provenance of datasets)

	Rv3142c/-	Rv2355/-
Fe_supp_jason_reseq	-0.278	0.044
low_pH_jason_reseq	-0.852	-0.564
NO_jason_reseq	0.399	0.158
B6_jason_reseq	-0.254	-0.298
MHCII_jason_reseq	-0.69	0.054
Isoniazid02	-0.172	0.047
Rifampicin4	0.317	1.018
Ethambutol3	0.116	0.416
Meropenem3	0.019	-0.135
Vancomycin16	0.26	0.013
Rv2680_day32	-0.971	-0.084
H37Rv_KO_MarP	-0.155	-0.285
hypoxia_3wks	0.024	0.419
hypoxia_6wks	-0.432	0.125
glycerol	-0.825	-0.866
cholesterol	0.155	-0.016
AJ	1.219	1.197
Bibs02	0.257	1.068
Bibs02c	1.422	1.675
BL6	0.821	0.217
BL6a	1.653	1.072
BXD01	0.919	0.643
BXD010	1.183	0.786
BXD011	1.105	0.752
BXD03	0.324	0.715
BXD04	0.606	0.455
BXD05	1.049	0.947
BXD06	0.946	0.431
BXD07	1.398	0.655
BXD08	0.626	0.538
BXD09	0.913	0.65
CAST	1.303	1.089
CCcont	0.784	0.177
DS01	0.79	0.972
DS02	0.521	1.007
DS04	0.512	1.317
DS0c	0.793	1.042
GP01	0.674	1.034
GP02	0.388	1.191
GP0c	0.362	0.53
NOD	1.084	1.318
NZO	0.64	0.984
PWK	1.186	1.098
H37Rv_KO_CtpC	1.517	0.752
H37Rv_KO_CtpD	1.639	0.953
H37Rv_KO_Rv1272	1.18	0.57
H37Rv_KO_SugABC	1.178	1.016
H37Rv_KO_MbtN	1.207	0.685
Trans05	1.301	0.851
macrophage_unactivated	0.104	-0.59
IL1	-0.872	-0.306
Rapamycin	-0.353	-0.335
Tcell	-0.186	-1.017
GMCSF	-0.655	-0.272
IFNab	-0.871	-0.729
IFNg	0.326	-0.428
IFNg_GMCSF1	-0.088	-0.226
Rv1432_day32	-0.061	0.492
Rv1565c_day32	0.204	0.278
secA2_input	0.059	-0.315
delta_Rv3594	-0.268	-0.153
delta_Rv3717	-0.294	-0.344
delta_Rv3811	0.092	-0.116
delta_Rv0954	-0.322	0.429
PonA1	0.167	0.0
EccD1_KO	-0.342	0.214
EspI_KO	0.211	0.676
PE35_KO	0.3	0.79
PPE68_KO	0.218	0.464
glycerol2	-0.092	-0.787
lignocerate	0.754	-0.553
oleate	-0.411	-0.871
phosphatidylcholine	-0.022	-0.774
acetate	0.213	-0.321
glucAc	0.495	-0.055
Rv0950ko	1.462	0.166
Rv1096ko	0.072	-0.018
Rv3684ko	0.229	-0.38
delta_otsA_trehalose	0.14	-0.173