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 Rv3511/PE_PGRS55:

update plot	correlation	link to info on gene
Rv0834c/PE_PGRS14	(cc=0.7185)	info on Rv0834c/PE_PGRS14
Rv3508/PE_PGRS54	(cc=0.6409)	info on Rv3508/PE_PGRS54
Rv3512/PE_PGRS56	(cc=0.5701)	info on Rv3512/PE_PGRS56
Rv0235c/-	(cc=0.5471)	info on Rv0235c/-
Rv3514/PE_PGRS57	(cc=0.5468)	info on Rv3514/PE_PGRS57
Rv3345c/PE_PGRS50	(cc=0.5418)	info on Rv3345c/PE_PGRS50
Rv1891/-	(cc=0.5372)	info on Rv1891/-
Rv0833/PE_PGRS13	(cc=0.5355)	info on Rv0833/PE_PGRS13
Rv3394c/-	(cc=0.5008)	info on Rv3394c/-
Rv0354c/PPE7	(cc=0.5006)	info on Rv0354c/PPE7

Correlation of Rv3511/PE_PGRS55 with Rv3345c/PE_PGRS50

Normalized LFCs for Rv3511/PE_PGRS55:
(description and provenance of datasets)

	Rv3511/PE_PGRS55	Rv3345c/PE_PGRS50
Fe_supp_jason_reseq	-0.718	-1.345
low_pH_jason_reseq	-0.269	-1.425
NO_jason_reseq	-0.278	-1.336
B6_jason_reseq	-0.682	-1.393
MHCII_jason_reseq	0.111	-0.765
Isoniazid02	-1.059	-1.269
Rifampicin4	0.444	0.306
Ethambutol3	-0.565	-0.062
Meropenem3	-0.213	0.059
Vancomycin16	-0.348	-0.679
Rv2680_day32	-0.922	0.323
H37Rv_KO_MarP	0.014	0.206
hypoxia_3wks	-0.618	0.662
hypoxia_6wks	-1.347	0.159
glycerol	0.686	0.97
cholesterol	0.429	0.435
AJ	0.844	0.845
Bibs02	-0.334	0.801
Bibs02c	0.685	0.946
BL6	-0.228	-1.081
BL6a	0.321	0.0
BXD01	0.31	0.392
BXD010	-0.196	-0.502
BXD011	-0.297	-0.54
BXD03	1.067	0.167
BXD04	0.287	0.431
BXD05	0.589	0.166
BXD06	0.178	-0.523
BXD07	0.41	-0.159
BXD08	0.632	0.356
BXD09	0.287	-0.422
CAST	0.075	-0.265
CCcont	-0.025	-0.842
DS01	-0.866	-0.577
DS02	-0.112	0.137
DS04	-0.083	-0.37
DS0c	-0.484	-0.991
GP01	0.579	0.375
GP02	1.313	0.846
GP0c	0.699	0.412
NOD	-0.322	0.638
NZO	1.052	0.126
PWK	0.374	0.388
H37Rv_KO_CtpC	0.561	-0.109
H37Rv_KO_CtpD	0.302	0.339
H37Rv_KO_Rv1272	0.058	0.304
H37Rv_KO_SugABC	0.649	0.083
H37Rv_KO_MbtN	0.319	1.406
Trans05	1.249	0.947
macrophage_unactivated	0.073	-0.514
IL1	-0.59	-2.011
Rapamycin	-0.611	-1.715
Tcell	-0.479	-1.466
GMCSF	0.544	0.069
IFNab	-0.683	-2.44
IFNg	-0.497	-0.93
IFNg_GMCSF1	-0.421	-0.698
Rv1432_day32	1.036	0.619
Rv1565c_day32	-0.524	-0.3
secA2_input	0.446	0.473
delta_Rv3594	-0.135	-0.167
delta_Rv3717	-0.53	-0.224
delta_Rv3811	-0.349	-0.373
delta_Rv0954	-0.808	-1.017
PonA1	0.0	-0.112
EccD1_KO	0.444	-0.385
EspI_KO	-0.225	-0.271
PE35_KO	-0.63	-0.61
PPE68_KO	-0.733	-0.669
glycerol2	0.248	0.085
lignocerate	0.342	-0.16
oleate	0.166	0.328
phosphatidylcholine	0.221	0.127
acetate	-0.057	0.514
glucAc	-0.023	0.124
Rv0950ko	0.609	0.166
Rv1096ko	0.531	0.232
Rv3684ko	-0.193	-0.426
delta_otsA_trehalose	-1.443	0.654