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 Rv2704/-:

update plot	correlation	link to info on gene
Rv1947/-	(cc=0.539)	info on Rv1947/-
Rv2389c/rpfD	(cc=0.4731)	info on Rv2389c/rpfD
Rv1770/-	(cc=0.4697)	info on Rv1770/-
Rv1000c/-	(cc=0.4429)	info on Rv1000c/-
Rv2067c/-	(cc=0.439)	info on Rv2067c/-
Rv2658c/-	(cc=0.4381)	info on Rv2658c/-
Rv0868c/moaD2	(cc=0.4188)	info on Rv0868c/moaD2
Rv3840/-	(cc=0.4148)	info on Rv3840/-
Rv0159c/PE3	(cc=0.4089)	info on Rv0159c/PE3
Rv2976c/ung	(cc=0.4081)	info on Rv2976c/ung

Correlation of Rv2704/- with Rv1000c/-

Normalized LFCs for Rv2704/-:
(description and provenance of datasets)

	Rv2704/-	Rv1000c/-
Fe_supp_jason_reseq	-0.524	-1.361
low_pH_jason_reseq	-1.223	-2.546
NO_jason_reseq	0.446	-0.197
B6_jason_reseq	0.083	-0.576
MHCII_jason_reseq	0.254	-0.576
Isoniazid02	-1.029	-1.963
Rifampicin4	0.449	0.384
Ethambutol3	-0.916	-1.688
Meropenem3	0.277	-1.517
Vancomycin16	0.0	-0.584
Rv2680_day32	-0.596	-1.602
H37Rv_KO_MarP	-0.439	0.138
hypoxia_3wks	0.195	0.06
hypoxia_6wks	-0.616	0.566
glycerol	0.151	0.127
cholesterol	0.028	0.507
AJ	-0.405	0.45
Bibs02	0.16	-0.091
Bibs02c	-0.291	0.073
BL6	0.321	0.353
BL6a	0.138	-0.324
BXD01	-0.276	-0.594
BXD010	0.537	0.196
BXD011	0.175	0.672
BXD03	0.16	0.287
BXD04	0.223	-0.76
BXD05	0.547	-0.145
BXD06	0.576	-0.125
BXD07	0.11	0.244
BXD08	-0.318	-0.345
BXD09	0.227	-0.379
CAST	0.184	-0.229
CCcont	-0.617	-0.888
DS01	-0.176	0.542
DS02	0.169	0.569
DS04	0.214	0.52
DS0c	0.064	0.608
GP01	0.087	0.172
GP02	0.714	0.497
GP0c	-0.067	-0.196
NOD	0.508	0.477
NZO	-0.65	0.458
PWK	0.279	-0.345
H37Rv_KO_CtpC	-0.051	0.211
H37Rv_KO_CtpD	-0.442	0.678
H37Rv_KO_Rv1272	0.57	-0.644
H37Rv_KO_SugABC	-0.426	1.463
H37Rv_KO_MbtN	0.21	0.647
Trans05	-0.687	-0.157
macrophage_unactivated	0.287	-0.199
IL1	0.727	0.789
Rapamycin	0.648	0.657
Tcell	0.251	0.235
GMCSF	1.035	1.751
IFNab	0.868	0.323
IFNg	0.663	1.475
IFNg_GMCSF1	0.553	1.335
Rv1432_day32	-0.01	1.551
Rv1565c_day32	-0.166	0.607
secA2_input	-0.069	-1.032
delta_Rv3594	-0.219	-0.413
delta_Rv3717	-0.306	-0.417
delta_Rv3811	-0.601	-0.587
delta_Rv0954	-0.705	-0.115
PonA1	-0.605	-0.262
EccD1_KO	0.069	1.447
EspI_KO	0.151	1.805
PE35_KO	0.245	0.732
PPE68_KO	-0.086	1.113
glycerol2	-0.021	-0.147
lignocerate	-0.347	-0.136
oleate	0.21	0.405
phosphatidylcholine	-0.325	0.21
acetate	-0.025	-0.82
glucAc	-1.153	-0.624
Rv0950ko	-0.145	0.22
Rv1096ko	-0.866	0.715
Rv3684ko	-0.206	-0.639
delta_otsA_trehalose	0.659	-0.104