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 Rv3198c/uvrD2:

update plot	correlation	link to info on gene
Rv3388/PE_PGRS52	(cc=0.4981)	info on Rv3388/PE_PGRS52
Rv3512/PE_PGRS56	(cc=0.4684)	info on Rv3512/PE_PGRS56
Rv3428c/-	(cc=0.4532)	info on Rv3428c/-
Rv0213c/-	(cc=0.4522)	info on Rv0213c/-
Rv0515/-	(cc=0.4202)	info on Rv0515/-
Rv0787/-	(cc=0.4037)	info on Rv0787/-
Rv0814c/sseC2	(cc=0.4002)	info on Rv0814c/sseC2
Rv0260c/-	(cc=0.3973)	info on Rv0260c/-
Rv0963c/-	(cc=0.3904)	info on Rv0963c/-
Rv0872c/PE_PGRS15	(cc=0.3889)	info on Rv0872c/PE_PGRS15

Correlation of Rv3198c/uvrD2 with Rv0814c/sseC2

Normalized LFCs for Rv3198c/uvrD2:
(description and provenance of datasets)

	Rv3198c/uvrD2	Rv0814c/sseC2
Fe_supp_jason_reseq	-0.096	1.257
low_pH_jason_reseq	-0.323	-1.021
NO_jason_reseq	-0.331	-0.449
B6_jason_reseq	0.604	-0.872
MHCII_jason_reseq	0.192	-0.833
Isoniazid02	-0.135	-0.704
Rifampicin4	-0.43	-0.244
Ethambutol3	-0.113	1.422
Meropenem3	0.628	0.426
Vancomycin16	0.157	-0.528
Rv2680_day32	-0.312	-1.282
H37Rv_KO_MarP	-0.185	-1.143
hypoxia_3wks	-0.387	-0.59
hypoxia_6wks	-0.497	-0.286
glycerol	0.282	-0.584
cholesterol	0.518	-0.013
AJ	0.899	1.035
Bibs02	0.709	1.461
Bibs02c	1.099	1.091
BL6	0.053	-0.327
BL6a	0.552	0.314
BXD01	0.081	0.642
BXD010	0.054	0.4
BXD011	0.475	0.711
BXD03	0.263	1.115
BXD04	0.15	1.163
BXD05	0.237	0.487
BXD06	0.135	0.724
BXD07	-0.446	0.637
BXD08	0.592	0.879
BXD09	0.322	0.203
CAST	0.752	3.372
CCcont	1.098	1.338
DS01	0.373	1.17
DS02	0.711	1.245
DS04	0.968	0.058
DS0c	0.22	0.476
GP01	-0.577	-0.619
GP02	0.629	-0.82
GP0c	-0.346	-0.785
NOD	0.552	0.867
NZO	1.402	0.149
PWK	0.641	0.662
H37Rv_KO_CtpC	-0.345	-0.049
H37Rv_KO_CtpD	1.436	0.825
H37Rv_KO_Rv1272	0.795	1.101
H37Rv_KO_SugABC	1.151	1.171
H37Rv_KO_MbtN	0.105	0.989
Trans05	0.525	1.089
macrophage_unactivated	0.186	-0.35
IL1	0.0	-1.163
Rapamycin	0.522	-0.316
Tcell	0.0	-1.206
GMCSF	0.449	0.108
IFNab	0.0	-0.311
IFNg	0.158	-0.083
IFNg_GMCSF1	-0.192	1.417
Rv1432_day32	0.541	-0.824
Rv1565c_day32	0.355	-0.229
secA2_input	0.0	0.149
delta_Rv3594	-0.379	-2.856
delta_Rv3717	-0.238	-3.69
delta_Rv3811	0.214	-3.123
delta_Rv0954	-0.963	-2.423
PonA1	-0.03	-3.053
EccD1_KO	0.293	-0.181
EspI_KO	-0.088	0.288
PE35_KO	-0.277	0.563
PPE68_KO	0.192	0.195
glycerol2	0.611	0.506
lignocerate	1.112	0.357
oleate	-0.549	0.838
phosphatidylcholine	0.611	0.65
acetate	0.618	1.538
glucAc	0.944	0.202
Rv0950ko	-0.247	-0.118
Rv1096ko	-0.513	-0.639
Rv3684ko	0.95	-1.339
delta_otsA_trehalose	1.056	-0.57