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 Rv2345/-:

update plot	correlation	link to info on gene
Rv1947/-	(cc=0.6789)	info on Rv1947/-
Rv1000c/-	(cc=0.6093)	info on Rv1000c/-
Rv1899c/lppD	(cc=0.6084)	info on Rv1899c/lppD
Rv1175c/fadH	(cc=0.5897)	info on Rv1175c/fadH
Rv2313c/-	(cc=0.5727)	info on Rv2313c/-
Rv2658c/-	(cc=0.5726)	info on Rv2658c/-
Rv0399c/lpqK	(cc=0.5689)	info on Rv0399c/lpqK
Rv2947c/pks15	(cc=0.5434)	info on Rv2947c/pks15
Rv2639c/-	(cc=0.541)	info on Rv2639c/-
Rv1857/modA	(cc=0.5206)	info on Rv1857/modA

Correlation of Rv2345/- with Rv2658c/-

Normalized LFCs for Rv2345/-:
(description and provenance of datasets)

	Rv2345/-	Rv2658c/-
Fe_supp_jason_reseq	-0.019	0.387
low_pH_jason_reseq	-0.962	-0.974
NO_jason_reseq	-0.053	0.0
B6_jason_reseq	-0.063	0.034
MHCII_jason_reseq	0.065	0.572
Isoniazid02	-1.199	-0.778
Rifampicin4	0.509	0.311
Ethambutol3	-1.019	-0.143
Meropenem3	-1.409	-1.622
Vancomycin16	-0.655	-1.059
Rv2680_day32	-0.466	-0.294
H37Rv_KO_MarP	-0.02	0.78
hypoxia_3wks	0.032	0.279
hypoxia_6wks	0.257	-0.186
glycerol	0.192	0.265
cholesterol	-0.086	0.041
AJ	0.0	-0.655
Bibs02	-0.278	0.229
Bibs02c	-0.205	0.391
BL6	0.138	-0.702
BL6a	0.118	0.564
BXD01	0.14	-0.257
BXD010	0.141	-0.135
BXD011	-0.262	-0.076
BXD03	-0.04	0.005
BXD04	0.291	-0.339
BXD05	0.374	0.775
BXD06	0.147	-0.034
BXD07	0.238	0.344
BXD08	0.434	-0.109
BXD09	0.199	0.098
CAST	-0.225	0.444
CCcont	0.024	-0.182
DS01	0.0	0.05
DS02	-0.498	0.307
DS04	-0.142	-0.197
DS0c	-0.057	0.732
GP01	0.277	-0.697
GP02	0.072	-0.467
GP0c	0.147	-0.551
NOD	0.265	0.664
NZO	-0.237	0.118
PWK	-0.058	0.448
H37Rv_KO_CtpC	0.373	-0.272
H37Rv_KO_CtpD	0.605	0.798
H37Rv_KO_Rv1272	0.291	0.35
H37Rv_KO_SugABC	0.767	0.476
H37Rv_KO_MbtN	0.628	0.685
Trans05	0.501	0.346
macrophage_unactivated	-0.114	0.309
IL1	0.338	0.653
Rapamycin	0.473	0.715
Tcell	0.039	-0.101
GMCSF	0.599	0.512
IFNab	0.311	0.435
IFNg	0.216	0.446
IFNg_GMCSF1	0.182	0.248
Rv1432_day32	0.194	0.037
Rv1565c_day32	0.175	0.125
secA2_input	0.233	-0.254
delta_Rv3594	0.271	-0.052
delta_Rv3717	0.055	-0.551
delta_Rv3811	0.352	-0.425
delta_Rv0954	0.371	0.133
PonA1	-0.321	-0.97
EccD1_KO	0.704	0.089
EspI_KO	0.767	0.893
PE35_KO	0.429	0.939
PPE68_KO	0.176	0.189
glycerol2	0.277	-0.472
lignocerate	0.284	-0.756
oleate	0.702	0.191
phosphatidylcholine	0.153	-0.282
acetate	-0.462	-0.233
glucAc	-0.232	-0.879
Rv0950ko	0.434	0.027
Rv1096ko	-0.567	-0.784
Rv3684ko	-0.54	-0.802
delta_otsA_trehalose	0.582	1.711