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 Rv2097c/pafA:

update plot	correlation	link to info on gene
Rv2115c/mpa	(cc=0.8805)	info on Rv2115c/mpa
Rv0412c/-	(cc=0.7896)	info on Rv0412c/-
Rv0410c/pknG	(cc=0.7427)	info on Rv0410c/pknG
Rv1685c/-	(cc=0.71)	info on Rv1685c/-
Rv2397c/cysA1	(cc=0.6933)	info on Rv2397c/cysA1
Rv3035/-	(cc=0.6545)	info on Rv3035/-
Rv2399c/cysT	(cc=0.6487)	info on Rv2399c/cysT
Rv0411c/glnH	(cc=0.6098)	info on Rv0411c/glnH
Rv1631/coaE	(cc=0.5935)	info on Rv1631/coaE
Rv2198c/mmpS3	(cc=0.5926)	info on Rv2198c/mmpS3

Correlation of Rv2097c/pafA with Rv2115c/mpa

Normalized LFCs for Rv2097c/pafA:
(description and provenance of datasets)

	Rv2097c/pafA	Rv2115c/mpa
Fe_supp_jason_reseq	0.415	0.766
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	1.104	0.953
Rifampicin4	-0.712	-0.149
Ethambutol3	-0.745	-1.608
Meropenem3	-0.876	-2.01
Vancomycin16	0.753	1.252
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-2.592	-2.406
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	-0.202	0.0
cholesterol	-0.145	0.0
AJ	-0.232	0.0
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	-0.125	0.0
BL6a	-0.198	0.0
BXD01	-0.13	0.0
BXD010	-0.128	0.0
BXD011	-0.127	0.35
BXD03	-0.135	0.0
BXD04	-0.124	0.0
BXD05	-0.135	0.0
BXD06	-0.133	0.0
BXD07	-0.138	0.0
BXD08	-0.133	0.0
BXD09	-0.14	0.0
CAST	-0.23	0.0
CCcont	1.667	2.042
DS01	-0.236	0.0
DS02	-0.217	0.0
DS04	0.0	0.37
DS0c	0.0	0.0
GP01	-0.099	0.099
GP02	-0.083	0.353
GP0c	-0.13	0.0
NOD	-0.225	0.0
NZO	-0.199	0.0
PWK	-0.196	0.0
H37Rv_KO_CtpC	-0.162	0.0
H37Rv_KO_CtpD	0.496	0.537
H37Rv_KO_Rv1272	-0.141	0.0
H37Rv_KO_SugABC	0.0	0.099
H37Rv_KO_MbtN	0.18	0.196
Trans05	-0.131	0.131
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	1.398	0.017
delta_Rv3594	-0.193	0.369
delta_Rv3717	-0.331	-0.174
delta_Rv3811	-0.391	0.187
delta_Rv0954	3.287	4.133
PonA1	3.848	5.436
EccD1_KO	-2.194	-0.549
EspI_KO	-2.284	0.493
PE35_KO	2.15	4.25
PPE68_KO	2.201	3.561
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.229	0.437
glucAc	0.0	0.701
Rv0950ko	-1.113	-1.842
Rv1096ko	-2.744	-4.189
Rv3684ko	-0.74	-1.055
delta_otsA_trehalose	-1.385	-0.374