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 Rv2998/-:

update plot	correlation	link to info on gene
Rv1508A/-	(cc=0.5325)	info on Rv1508A/-
Rv2492/-	(cc=0.5168)	info on Rv2492/-
Rv0691c/-	(cc=0.5138)	info on Rv0691c/-
Rv3138/pflA	(cc=0.5123)	info on Rv3138/pflA
Rv0567/-	(cc=0.4873)	info on Rv0567/-
Rv2310/-	(cc=0.4857)	info on Rv2310/-
Rv1269c/-	(cc=0.4854)	info on Rv1269c/-
Rv2880c/-	(cc=0.4774)	info on Rv2880c/-
Rv0934/pstS1	(cc=0.4497)	info on Rv0934/pstS1
Rv0557/mgtA	(cc=0.4462)	info on Rv0557/mgtA

Correlation of Rv2998/- with Rv3138/pflA

Normalized LFCs for Rv2998/-:
(description and provenance of datasets)

	Rv2998/-	Rv3138/pflA
Fe_supp_jason_reseq	0.0	-0.298
low_pH_jason_reseq	-1.074	0.089
NO_jason_reseq	0.378	-0.06
B6_jason_reseq	-0.74	-0.658
MHCII_jason_reseq	0.621	-0.094
Isoniazid02	-0.723	0.153
Rifampicin4	0.647	-0.173
Ethambutol3	-0.373	0.358
Meropenem3	-1.329	-0.818
Vancomycin16	-0.568	-0.485
Rv2680_day32	-2.766	-0.696
H37Rv_KO_MarP	0.401	0.346
hypoxia_3wks	0.044	-0.032
hypoxia_6wks	0.67	-0.081
glycerol	-0.357	-0.575
cholesterol	-0.07	0.068
AJ	-0.015	0.425
Bibs02	-0.558	0.527
Bibs02c	0.571	0.582
BL6	0.368	0.17
BL6a	0.927	0.732
BXD01	0.66	0.703
BXD010	-0.018	0.479
BXD011	0.008	2.15
BXD03	0.289	0.39
BXD04	0.389	0.702
BXD05	1.214	0.833
BXD06	0.642	0.587
BXD07	0.769	0.831
BXD08	0.684	0.054
BXD09	0.576	0.746
CAST	0.137	-0.132
CCcont	-0.389	0.454
DS01	-0.536	0.0
DS02	-0.438	0.269
DS04	-0.208	-0.571
DS0c	1.571	0.36
GP01	1.334	0.456
GP02	-0.538	0.077
GP0c	-0.23	-0.103
NOD	-0.174	-0.212
NZO	-0.663	0.678
PWK	0.993	0.772
H37Rv_KO_CtpC	0.613	-0.241
H37Rv_KO_CtpD	1.171	-0.198
H37Rv_KO_Rv1272	0.714	0.362
H37Rv_KO_SugABC	-1.841	-0.155
H37Rv_KO_MbtN	-1.256	-0.113
Trans05	0.127	0.469
macrophage_unactivated	0.877	1.275
IL1	0.068	0.736
Rapamycin	0.071	0.292
Tcell	0.345	0.489
GMCSF	1.085	0.57
IFNab	0.121	0.133
IFNg	0.535	0.454
IFNg_GMCSF1	0.214	0.877
Rv1432_day32	1.7	0.159
Rv1565c_day32	-0.381	0.224
secA2_input	-0.304	-0.366
delta_Rv3594	-2.168	-0.878
delta_Rv3717	-1.986	-0.943
delta_Rv3811	-1.698	-0.665
delta_Rv0954	-1.265	0.12
PonA1	-2.401	-0.459
EccD1_KO	1.214	0.98
EspI_KO	0.633	0.268
PE35_KO	1.896	0.274
PPE68_KO	1.609	0.358
glycerol2	0.371	0.156
lignocerate	-0.186	0.379
oleate	0.74	0.021
phosphatidylcholine	0.577	0.328
acetate	-0.977	-0.286
glucAc	-1.121	-0.017
Rv0950ko	0.757	0.28
Rv1096ko	1.707	0.13
Rv3684ko	-0.242	0.616
delta_otsA_trehalose	-2.389	0.181