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 Rv1947/-

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

	Rv2345/-	Rv1947/-
Fe_supp_jason_reseq	-0.019	-0.837
low_pH_jason_reseq	-0.962	-1.733
NO_jason_reseq	-0.053	-0.557
B6_jason_reseq	-0.063	-0.522
MHCII_jason_reseq	0.065	-0.579
Isoniazid02	-1.199	-3.635
Rifampicin4	0.509	0.36
Ethambutol3	-1.019	-3.496
Meropenem3	-1.409	-2.943
Vancomycin16	-0.655	-1.727
Rv2680_day32	-0.466	-0.791
H37Rv_KO_MarP	-0.02	-0.776
hypoxia_3wks	0.032	0.239
hypoxia_6wks	0.257	-0.182
glycerol	0.192	-0.575
cholesterol	-0.086	-0.088
AJ	0.0	0.37
Bibs02	-0.278	0.156
Bibs02c	-0.205	0.406
BL6	0.138	0.333
BL6a	0.118	0.234
BXD01	0.14	0.359
BXD010	0.141	1.362
BXD011	-0.262	0.022
BXD03	-0.04	1.131
BXD04	0.291	0.618
BXD05	0.374	0.617
BXD06	0.147	0.74
BXD07	0.238	0.49
BXD08	0.434	0.143
BXD09	0.199	0.431
CAST	-0.225	0.053
CCcont	0.024	-0.335
DS01	0.0	-0.267
DS02	-0.498	-1.111
DS04	-0.142	0.443
DS0c	-0.057	0.506
GP01	0.277	-0.715
GP02	0.072	-1.404
GP0c	0.147	0.842
NOD	0.265	-0.623
NZO	-0.237	-0.998
PWK	-0.058	-0.301
H37Rv_KO_CtpC	0.373	0.966
H37Rv_KO_CtpD	0.605	0.688
H37Rv_KO_Rv1272	0.291	-0.413
H37Rv_KO_SugABC	0.767	2.349
H37Rv_KO_MbtN	0.628	-0.395
Trans05	0.501	0.558
macrophage_unactivated	-0.114	1.004
IL1	0.338	0.958
Rapamycin	0.473	1.897
Tcell	0.039	0.844
GMCSF	0.599	1.36
IFNab	0.311	2.143
IFNg	0.216	1.451
IFNg_GMCSF1	0.182	2.046
Rv1432_day32	0.194	-1.632
Rv1565c_day32	0.175	-0.303
secA2_input	0.233	0.011
delta_Rv3594	0.271	0.076
delta_Rv3717	0.055	0.143
delta_Rv3811	0.352	0.718
delta_Rv0954	0.371	-1.416
PonA1	-0.321	0.048
EccD1_KO	0.704	-0.506
EspI_KO	0.767	-0.074
PE35_KO	0.429	0.65
PPE68_KO	0.176	0.179
glycerol2	0.277	0.063
lignocerate	0.284	-0.9
oleate	0.702	1.014
phosphatidylcholine	0.153	-0.123
acetate	-0.462	-1.401
glucAc	-0.232	-2.763
Rv0950ko	0.434	-0.615
Rv1096ko	-0.567	-2.069
Rv3684ko	-0.54	-2.168
delta_otsA_trehalose	0.582	3.544