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 Rv1196/PPE18:

update plot	correlation	link to info on gene
Rv1194c/-	(cc=0.6576)	info on Rv1194c/-
Rv1195/PE13	(cc=0.6444)	info on Rv1195/PE13
Rv1872c/lldD2	(cc=0.5814)	info on Rv1872c/lldD2
Rv3223c/sigH	(cc=0.5787)	info on Rv3223c/sigH
Rv1364c/-	(cc=0.5578)	info on Rv1364c/-
Rv3152/nuoH	(cc=0.5339)	info on Rv3152/nuoH
Rv2107/PE22	(cc=0.5322)	info on Rv2107/PE22
Rv2814c/-	(cc=0.5308)	info on Rv2814c/-
Rv2479c/-	(cc=0.5303)	info on Rv2479c/-
Rv2106/-	(cc=0.5263)	info on Rv2106/-

Correlation of Rv1196/PPE18 with Rv1195/PE13

Normalized LFCs for Rv1196/PPE18:
(description and provenance of datasets)

	Rv1196/PPE18	Rv1195/PE13
Fe_supp_jason_reseq	-0.06	-0.235
low_pH_jason_reseq	-1.091	-0.44
NO_jason_reseq	-0.914	-1.37
B6_jason_reseq	-1.217	-1.208
MHCII_jason_reseq	0.228	0.977
Isoniazid02	2.462	1.176
Rifampicin4	0.842	-0.173
Ethambutol3	1.445	-0.304
Meropenem3	-0.121	-0.598
Vancomycin16	0.531	0.541
Rv2680_day32	-1.276	-0.383
H37Rv_KO_MarP	-0.934	-0.409
hypoxia_3wks	0.626	-0.307
hypoxia_6wks	0.875	-0.551
glycerol	0.828	0.323
cholesterol	0.379	-0.305
AJ	1.657	0.978
Bibs02	0.685	0.742
Bibs02c	1.155	0.653
BL6	1.282	0.175
BL6a	1.591	0.819
BXD01	0.97	0.097
BXD010	0.644	0.662
BXD011	1.367	0.268
BXD03	1.557	0.752
BXD04	0.999	0.517
BXD05	1.494	1.781
BXD06	0.919	-0.066
BXD07	0.923	0.264
BXD08	1.004	0.318
BXD09	1.004	0.604
CAST	0.863	0.971
CCcont	1.275	0.846
DS01	1.246	2.028
DS02	0.892	0.591
DS04	1.684	1.785
DS0c	1.171	1.782
GP01	0.765	1.288
GP02	0.418	0.829
GP0c	0.506	1.725
NOD	0.133	2.244
NZO	0.761	1.328
PWK	0.999	1.098
H37Rv_KO_CtpC	-0.175	-1.206
H37Rv_KO_CtpD	1.298	-0.295
H37Rv_KO_Rv1272	1.113	1.497
H37Rv_KO_SugABC	1.499	0.984
H37Rv_KO_MbtN	1.065	-0.5
Trans05	0.993	1.406
macrophage_unactivated	0.246	-0.022
IL1	-1.16	-1.774
Rapamycin	-0.35	0.021
Tcell	-1.0	-2.832
GMCSF	-0.742	-0.14
IFNab	1.62	1.49
IFNg	-1.868	-1.419
IFNg_GMCSF1	-0.308	-1.298
Rv1432_day32	-0.271	-0.18
Rv1565c_day32	-0.101	0.84
secA2_input	-0.312	0.546
delta_Rv3594	0.569	0.37
delta_Rv3717	0.865	-0.507
delta_Rv3811	0.758	0.397
delta_Rv0954	0.339	-0.881
PonA1	-0.369	-1.159
EccD1_KO	0.122	-0.345
EspI_KO	1.32	0.516
PE35_KO	0.72	-0.723
PPE68_KO	0.157	-1.635
glycerol2	1.103	0.17
lignocerate	0.742	-0.258
oleate	-0.425	-1.796
phosphatidylcholine	1.064	0.252
acetate	-0.045	-0.863
glucAc	0.176	-1.286
Rv0950ko	-0.057	-0.066
Rv1096ko	-0.03	-0.54
Rv3684ko	-0.226	-0.442
delta_otsA_trehalose	1.263	0.573