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 Rv0787/-

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

	Rv3198c/uvrD2	Rv0787/-
Fe_supp_jason_reseq	-0.096	-0.535
low_pH_jason_reseq	-0.323	-0.134
NO_jason_reseq	-0.331	-0.638
B6_jason_reseq	0.604	-0.345
MHCII_jason_reseq	0.192	1.042
Isoniazid02	-0.135	0.649
Rifampicin4	-0.43	0.073
Ethambutol3	-0.113	0.333
Meropenem3	0.628	0.447
Vancomycin16	0.157	0.072
Rv2680_day32	-0.312	-0.091
H37Rv_KO_MarP	-0.185	0.763
hypoxia_3wks	-0.387	-1.208
hypoxia_6wks	-0.497	-1.063
glycerol	0.282	1.731
cholesterol	0.518	0.663
AJ	0.899	-0.255
Bibs02	0.709	1.207
Bibs02c	1.099	1.613
BL6	0.053	0.606
BL6a	0.552	0.894
BXD01	0.081	0.092
BXD010	0.054	-0.85
BXD011	0.475	0.09
BXD03	0.263	-0.82
BXD04	0.15	-0.355
BXD05	0.237	-0.502
BXD06	0.135	-0.478
BXD07	-0.446	-0.305
BXD08	0.592	-0.243
BXD09	0.322	-0.422
CAST	0.752	-0.999
CCcont	1.098	0.781
DS01	0.373	1.001
DS02	0.711	0.507
DS04	0.968	1.248
DS0c	0.22	1.065
GP01	-0.577	0.601
GP02	0.629	1.418
GP0c	-0.346	0.865
NOD	0.552	0.225
NZO	1.402	0.199
PWK	0.641	-1.421
H37Rv_KO_CtpC	-0.345	0.723
H37Rv_KO_CtpD	1.436	1.164
H37Rv_KO_Rv1272	0.795	0.799
H37Rv_KO_SugABC	1.151	1.242
H37Rv_KO_MbtN	0.105	0.214
Trans05	0.525	1.886
macrophage_unactivated	0.186	0.331
IL1	0.0	0.157
Rapamycin	0.522	-0.043
Tcell	0.0	0.661
GMCSF	0.449	-0.623
IFNab	0.0	0.822
IFNg	0.158	0.176
IFNg_GMCSF1	-0.192	-0.544
Rv1432_day32	0.541	1.275
Rv1565c_day32	0.355	0.853
secA2_input	0.0	0.302
delta_Rv3594	-0.379	-0.107
delta_Rv3717	-0.238	-0.717
delta_Rv3811	0.214	-0.489
delta_Rv0954	-0.963	-0.287
PonA1	-0.03	-0.78
EccD1_KO	0.293	0.5
EspI_KO	-0.088	0.799
PE35_KO	-0.277	0.195
PPE68_KO	0.192	0.71
glycerol2	0.611	0.366
lignocerate	1.112	1.59
oleate	-0.549	-0.791
phosphatidylcholine	0.611	1.618
acetate	0.618	1.032
glucAc	0.944	1.303
Rv0950ko	-0.247	-0.476
Rv1096ko	-0.513	-0.416
Rv3684ko	0.95	-0.815
delta_otsA_trehalose	1.056	0.522