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 Rv3305c/amiA1:

update plot	correlation	link to info on gene
Rv1664/pks9	(cc=0.5626)	info on Rv1664/pks9
Rv2190c/-	(cc=0.5293)	info on Rv2190c/-
Rv2179c/-	(cc=0.5248)	info on Rv2179c/-
Rv2584c/apt	(cc=0.5186)	info on Rv2584c/apt
Rv2519/PE26	(cc=0.5142)	info on Rv2519/PE26
Rv2352c/PPE38	(cc=0.5087)	info on Rv2352c/PPE38
Rv3864/espE	(cc=0.5063)	info on Rv3864/espE
Rv1420/uvrC	(cc=0.4914)	info on Rv1420/uvrC
Rv2886c/-	(cc=0.4886)	info on Rv2886c/-
Rv3750c/-	(cc=0.4825)	info on Rv3750c/-

Correlation of Rv3305c/amiA1 with Rv2352c/PPE38

Normalized LFCs for Rv3305c/amiA1:
(description and provenance of datasets)

	Rv3305c/amiA1	Rv2352c/PPE38
Fe_supp_jason_reseq	-1.711	0.35
low_pH_jason_reseq	-2.014	-1.029
NO_jason_reseq	-0.454	-0.491
B6_jason_reseq	-1.483	-0.488
MHCII_jason_reseq	0.372	-0.46
Isoniazid02	-1.007	-1.043
Rifampicin4	0.062	-0.208
Ethambutol3	-0.337	-0.882
Meropenem3	-1.118	-1.085
Vancomycin16	-1.374	-0.602
Rv2680_day32	0.595	-0.611
H37Rv_KO_MarP	-0.449	-0.629
hypoxia_3wks	-1.252	-0.06
hypoxia_6wks	0.814	-0.56
glycerol	2.099	0.532
cholesterol	1.663	0.575
AJ	0.255	0.321
Bibs02	1.099	0.203
Bibs02c	-0.55	0.297
BL6	0.882	0.173
BL6a	0.0	0.425
BXD01	1.316	0.346
BXD010	-0.337	-0.031
BXD011	0.226	-0.232
BXD03	0.657	0.503
BXD04	1.303	0.661
BXD05	0.78	0.358
BXD06	0.941	0.167
BXD07	0.456	0.22
BXD08	1.626	0.298
BXD09	0.614	0.376
CAST	0.172	0.235
CCcont	2.22	-0.032
DS01	0.778	0.267
DS02	-0.922	0.17
DS04	1.036	0.554
DS0c	0.313	0.179
GP01	0.527	0.253
GP02	-0.705	0.349
GP0c	0.231	0.348
NOD	0.324	-0.184
NZO	-0.733	0.393
PWK	-0.242	0.06
H37Rv_KO_CtpC	0.79	0.169
H37Rv_KO_CtpD	1.37	0.659
H37Rv_KO_Rv1272	1.885	1.248
H37Rv_KO_SugABC	0.956	0.005
H37Rv_KO_MbtN	0.747	0.457
Trans05	1.413	1.088
macrophage_unactivated	1.613	0.511
IL1	0.107	-0.11
Rapamycin	0.988	0.037
Tcell	1.323	-0.495
GMCSF	1.669	0.533
IFNab	-0.112	0.054
IFNg	-0.299	0.088
IFNg_GMCSF1	0.0	0.364
Rv1432_day32	0.117	0.407
Rv1565c_day32	1.039	-0.141
secA2_input	-1.781	-0.626
delta_Rv3594	1.173	0.583
delta_Rv3717	0.593	-0.374
delta_Rv3811	0.561	0.268
delta_Rv0954	-0.067	0.289
PonA1	0.085	0.085
EccD1_KO	-0.477	-0.566
EspI_KO	-0.174	-0.031
PE35_KO	-0.554	0.105
PPE68_KO	-1.84	0.275
glycerol2	0.252	0.167
lignocerate	-0.387	-0.169
oleate	-1.229	-0.004
phosphatidylcholine	-1.535	-0.224
acetate	-1.006	-0.047
glucAc	-1.159	0.016
Rv0950ko	-1.155	0.277
Rv1096ko	-0.148	-0.012
Rv3684ko	-1.153	-0.134
delta_otsA_trehalose	1.247	0.184