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 Rv0479c/-:

update plot	correlation	link to info on gene
Rv1410c/-	(cc=0.4901)	info on Rv1410c/-
Rv2581c/-	(cc=0.4775)	info on Rv2581c/-
Rv2334/cysK1	(cc=0.4572)	info on Rv2334/cysK1
Rv2793c/truB	(cc=0.4569)	info on Rv2793c/truB
Rv1254/-	(cc=0.4554)	info on Rv1254/-
Rv0563/htpX	(cc=0.4508)	info on Rv0563/htpX
Rv2195/qcrA	(cc=0.4359)	info on Rv2195/qcrA
Rv0017c/rodA	(cc=0.4297)	info on Rv0017c/rodA
Rv2207/cobT	(cc=0.4225)	info on Rv2207/cobT
Rv1498c/-	(cc=0.4196)	info on Rv1498c/-

Correlation of Rv0479c/- with Rv1254/-

Normalized LFCs for Rv0479c/-:
(description and provenance of datasets)

	Rv0479c/-	Rv1254/-
Fe_supp_jason_reseq	1.047	0.0
low_pH_jason_reseq	2.13	0.0
NO_jason_reseq	-0.331	0.0
B6_jason_reseq	-0.292	0.0
MHCII_jason_reseq	-0.257	0.135
Isoniazid02	0.311	-0.183
Rifampicin4	-1.283	-0.341
Ethambutol3	-0.676	-0.32
Meropenem3	-0.883	-0.151
Vancomycin16	-1.257	-0.334
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.696	-0.684
hypoxia_3wks	-0.55	0.0
hypoxia_6wks	-0.288	0.0
glycerol	0.856	0.202
cholesterol	0.398	0.398
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.574
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.525	0.0
DS01	0.0	0.236
DS02	0.0	0.217
DS04	0.0	0.533
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.688	0.0
H37Rv_KO_CtpD	0.445	0.0
H37Rv_KO_Rv1272	0.693	0.0
H37Rv_KO_SugABC	0.863	0.0
H37Rv_KO_MbtN	0.196	0.0
Trans05	0.642	0.0
macrophage_unactivated	-0.398	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	-0.694	0.0
IFNab	-0.381	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	-0.396	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.218
secA2_input	0.25	-0.412
delta_Rv3594	-1.459	-1.427
delta_Rv3717	0.113	1.258
delta_Rv3811	-0.836	-0.454
delta_Rv0954	-1.769	-1.206
PonA1	-0.054	-1.235
EccD1_KO	0.664	0.0
EspI_KO	0.75	0.0
PE35_KO	0.939	0.767
PPE68_KO	-0.237	0.442
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.229	0.0
glucAc	0.272	0.0
Rv0950ko	2.044	0.0
Rv1096ko	0.793	0.0
Rv3684ko	0.0	0.0
delta_otsA_trehalose	-0.431	0.133