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 Rv2658c/-

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

	Rv2704/-	Rv2658c/-
Fe_supp_jason_reseq	-0.524	0.387
low_pH_jason_reseq	-1.223	-0.974
NO_jason_reseq	0.446	0.0
B6_jason_reseq	0.083	0.034
MHCII_jason_reseq	0.254	0.572
Isoniazid02	-1.029	-0.778
Rifampicin4	0.449	0.311
Ethambutol3	-0.916	-0.143
Meropenem3	0.277	-1.622
Vancomycin16	0.0	-1.059
Rv2680_day32	-0.596	-0.294
H37Rv_KO_MarP	-0.439	0.78
hypoxia_3wks	0.195	0.279
hypoxia_6wks	-0.616	-0.186
glycerol	0.151	0.265
cholesterol	0.028	0.041
AJ	-0.405	-0.655
Bibs02	0.16	0.229
Bibs02c	-0.291	0.391
BL6	0.321	-0.702
BL6a	0.138	0.564
BXD01	-0.276	-0.257
BXD010	0.537	-0.135
BXD011	0.175	-0.076
BXD03	0.16	0.005
BXD04	0.223	-0.339
BXD05	0.547	0.775
BXD06	0.576	-0.034
BXD07	0.11	0.344
BXD08	-0.318	-0.109
BXD09	0.227	0.098
CAST	0.184	0.444
CCcont	-0.617	-0.182
DS01	-0.176	0.05
DS02	0.169	0.307
DS04	0.214	-0.197
DS0c	0.064	0.732
GP01	0.087	-0.697
GP02	0.714	-0.467
GP0c	-0.067	-0.551
NOD	0.508	0.664
NZO	-0.65	0.118
PWK	0.279	0.448
H37Rv_KO_CtpC	-0.051	-0.272
H37Rv_KO_CtpD	-0.442	0.798
H37Rv_KO_Rv1272	0.57	0.35
H37Rv_KO_SugABC	-0.426	0.476
H37Rv_KO_MbtN	0.21	0.685
Trans05	-0.687	0.346
macrophage_unactivated	0.287	0.309
IL1	0.727	0.653
Rapamycin	0.648	0.715
Tcell	0.251	-0.101
GMCSF	1.035	0.512
IFNab	0.868	0.435
IFNg	0.663	0.446
IFNg_GMCSF1	0.553	0.248
Rv1432_day32	-0.01	0.037
Rv1565c_day32	-0.166	0.125
secA2_input	-0.069	-0.254
delta_Rv3594	-0.219	-0.052
delta_Rv3717	-0.306	-0.551
delta_Rv3811	-0.601	-0.425
delta_Rv0954	-0.705	0.133
PonA1	-0.605	-0.97
EccD1_KO	0.069	0.089
EspI_KO	0.151	0.893
PE35_KO	0.245	0.939
PPE68_KO	-0.086	0.189
glycerol2	-0.021	-0.472
lignocerate	-0.347	-0.756
oleate	0.21	0.191
phosphatidylcholine	-0.325	-0.282
acetate	-0.025	-0.233
glucAc	-1.153	-0.879
Rv0950ko	-0.145	0.027
Rv1096ko	-0.866	-0.784
Rv3684ko	-0.206	-0.802
delta_otsA_trehalose	0.659	1.711