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“noisy” signal analysis

Published byEmery Beasley Modified over 7 years ago

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Presentation on theme: "“noisy” signal analysis"— Presentation transcript:

1 “noisy” signal analysis
DRS data: “noisy” signal analysis

2 Signal vs. “noisy” signal
Several replicas allow a noise level estimation: if a site have reads in one replica and does not have ones in other replicas it is a “dubious” noise site. We can/should/must exclude the site from consideration. Here we follow another prescription: hard cut Join replicas into one data set Build bins (3 nts per bin) Normalise data Choose bins with a cut (Nreads > 4.0 norm. reads): signal bins Find genes (TAIR9 gene +/- 25 nts) with signal bins Nreads > 5.0 “Noisy” signal Arabidopsis Project Dundee, 29/06/2010

3 DRS data statistics WT sample (2 biological replicas):
Nreads= Kreads; Data normalized: 6.6 real reads correspond to 1 norm. read! Nsites= Ksites (Nbin= 3 nts); Nsites= signal sites (Nreads > 4.0 norm. reads) 7459 expressed genes (Nreads > 5.0) FPAox sample (3 biological replicas): Nreads= Kreads; Nsites= Ksites (Nbin= 3 nts); signal sites (Nreads > 4.0 norm. reads) 7357 expressed genes fpa-8 sample (3 biological replicas): Nreads = Kreads; Nsites= Ksites (Nbin= 3 nts); signal sites 7010 expressed genes Arabidopsis Project Dundee, 29/06/2010

4 Expressed TAIR9 genes Arabidopsis Project Dundee, 29/06/2010

5 Analysis Build bins and select “noisy” signal bins in 3 data sets: WT, FPAox, fpa-8 Select expressed genes Analyse differential expressions in 3 data sets Select genes, which are expressed in all 3 datasets Select genes, which are expressed in 2 datasets Select genes, which are expressed in 1 dataset only Apply cuts for these gene sets Down-regulated in FPAox and up-regulated in fpa8 for (1) and (2) Up-regulated both in FPAox and fpa8 for (3) Arabidopsis Project Dundee, 29/06/2010

6 All expressed genes in all 3 samples (log scale): 6293 genes
Expressed TAIR9 genes All expressed genes in all 3 samples (log scale): 6293 genes Arabidopsis Project Dundee, 29/06/2010

7 Lets add gene identifiers. Mess...
Expressed TAIR9 genes Lets add gene identifiers. Mess... Arabidopsis Project Dundee, 29/06/2010

8 Lets apply a condition: down-reg. FPAox and up-reg. fpa8
Expressed TAIR9 genes Lets apply a condition: down-reg. FPAox and up-reg. fpa8 Arabidopsis Project Dundee, 29/06/2010

9 Genes in (2) and (3): expressed in 1/2 data sets. 1965 genes
Expressed TAIR9 genes Genes in (2) and (3): expressed in 1/2 data sets genes Arabidopsis Project Dundee, 29/06/2010

10 Lets remove genes expressed in 1 data set only
Expressed TAIR9 genes Lets remove genes expressed in 1 data set only Arabidopsis Project Dundee, 29/06/2010

11 … and apply the same condition → 8 genes
Expressed TAIR9 genes … and apply the same condition → 8 genes Arabidopsis Project Dundee, 29/06/2010

12 A distribution of genes expressed in one sample only
Expressed TAIR9 genes A distribution of genes expressed in one sample only Arabidopsis Project Dundee, 29/06/2010

13 Expressed TAIR9 genes Set a cut → 13 genes Dundee, 29/06/2010
Arabidopsis Project Dundee, 29/06/2010

14 List of expressed genes
Expressed genes in all three datasets (condition: FPAox/WT < 1.0 and fpa8/WT > 2.0) AT1G PAP3 (PURPLE ACID PHOSPHATASE 3) AT1G protein coding: unknown protein AT1G protein coding: monodehydroascorbate reductase AT1G SOT18 (DESULFO-GLUCOSINOLATE SULFOTRANSFERASE 18) AT1G protein coding: glycerophosphoryl diester phosphodiesterase family protein AT1G Aty2 (Arabidopsis thioredoxin y2) AT2G ATVSR3 (ARABIDOPSIS THALIANA VACULOLAR SORTING RECEPTOR 3) AT2G HPT1 (HOMOGENTISATE PHYTYLTRANSFERASE 1) AT2G BGLU33 (BETA GLUCOSIDASE 33) AT2G protein coding: AAA-type ATPase family protein AT3G protein coding: ATP binding / microtubule motor AT3G AOC2 (ALLENE OXIDE CYCLASE 2) AT3G CYP71A22 AT3G BGLU8 (BETA GLUCOSIDASE 8) AT3G ICL (ISOCITRATE LYASE) AT3G protein coding: unknown protein AT3G TT5 (TRANSPARENT TESTA 5) AT4G protein coding: plastid-lipid associated protein PAP / fibrillin family protein AT4G BAM5 (BETA-AMYLASE 5) AT4G protein coding: adenylosuccinate lyase, putative / adenylosuccinase, putative AT5G protein coding: 3-isopropylmalate dehydrogenase, chloroplast, putative AT5G SQE6 (SQUALENE MONOXYGENASE 6) Arabidopsis Project Dundee, 29/06/2010

15 List of expressed genes (2)
Expressed genes in two datasets (condition: FPAox/WT < 1.0 and fpa8/WT > 2.0) AT2G protein coding: NPL4 family protein AT2G CYP76C1 AT3G SCPL7 (SERINE CARBOXYPEPTIDASE-LIKE 7) AT3G protein coding: unknown protein AT5G LRR1 AT5G FLS2 (FLAGELLIN-SENSITIVE 2) AT5G protein coding: importin beta-2, putative AT5G protein coding: integral membrane HPP family protein Expressed genes in one dataset only (condition: FPAox/WT > 10.0 or fpa8/WT > 10.0) AT1G WAK1 (CELL WALL-ASSOCIATED KINASE) AT1G protein_coding: serine-type endopeptidase inhibitor AT2G protein_coding: unknown protein AT2G FPA AT2G protein_coding: chitinase, putative AT2G protein_coding: chitinase, putative AT3G QQS (QUA-QUINE STARCH) AT3G BGL2 (BETA-1,3-GLUCANASE 2) AT4G protein_coding: 2S seed storage protein 1 / 2S albumin storage protein / NWMU1-2S albumin 1 AT4G AT2S3 AT4G CRU3 (CRUCIFERIN 3) AT5G FLC (FLOWERING LOCUS C) AT5G protein_coding: protein kinase family protein Arabidopsis Project Dundee, 29/06/2010

16 List of expressed genes (3)
Expressed genes in three datasets (condition: FPAox/WT > 2.0 and fpa8/WT < 1.0) AT1G GSTF7 AT1G protein: enoyl-CoA hydratase/isomerase family protein AT1G undefined AT1G protein: unknown protein AT1G FMO GS-OX2 (FLAVIN-MONOOXYGENASE GLUCOSINOLATE S-OXYGENASE 2) AT1G protein: unknown protein AT1G HTH (HOTHEAD) AT2G protein: translin family protein AT2G RLK (receptor lectin kinase) AT2G protein: calmodulin-like calcium-binding protein, 22 kDa (CaBP-22) AT3G SYP121 (SYNTAXIN OF PLANTS 121) AT3G CYP71B22 AT3G ADT4 (arogenate dehydratase 4) AT3G SYP122 (SYNTAXIN OF PLANTS 122) AT4G ATGSTF2 (GLUTATHIONE S-TRANSFERASE PHI 2) AT4G MAPKKK10 AT4G protein: protease inhibitor/seed storage/lipid transfer protein (LTP) family protein AT4G protein: peptidyl-prolyl cis-trans isomerase AT4G protein: zinc finger (GATA type) family protein AT4G XTR6 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 6) AT5G CYP705A5 AT5G protein: leucine-rich repeat family protein / protein kinase family protein AT5G protein: peroxidase, putative Arabidopsis Project Dundee, 29/06/2010

17 List of expressed genes (4)
Expressed genes in two datasets (condition: FPAox/WT > 2.0 and fpa8/WT < 1.0) AT1G protein: glycine-rich protein AT1G ASB1 (ANTHRANILATE SYNTHASE BETA SUBUNIT 1) AT1G STZ (salt tolerance zinc finger) AT1G protein: protein phosphatase 2C, putative / PP2C, putative AT1G TOM6 (translocase of the outer mitochondrial membrane 6) AT1G protein: unknown protein AT1G protein: oxidoreductase, acting on the CH-CH group of donors AT1G protein: hydrolase, alpha/beta fold family protein AT2G protein: indole-3-glycerol phosphate synthase (IGPS) AT2G PR1 (PATHOGENESIS-RELATED GENE 1) AT2G protein: unknown protein AT2G AR781 AT2G WRKY25 AT2G protein: leucine-rich repeat transmembrane protein kinase, putative AT2G protein: 33 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putative AT2G protein: sugar transporter, putative AT3G protein: small nuclear ribonucleoprotein D1, putative / snRNP core protein D1, putative AT3G protein: unknown protein AT3G CYP71B24 AT3G protein: protein kinase-related AT3G WRKY70 AT5G protein: unknown protein AT5G protein: NADP-dependent oxidoreductase, putative AT5G protein: unknown protein AT5G protein: 33 kDa secretory protein-related AT5G protein: protease inhibitor/seed storage/lipid transfer protein (LTP) family protein AT5G protein: ethylene-responsive element-binding family protein AT5G protein: octicosapeptide/Phox/Bem1p (PB1) domain-containing protein Arabidopsis Project Dundee, 29/06/2010

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