Human Chromosomes frequencies
Vernone Annamaria

Author: Annamaria Vernone
Date: 08/01/2013

Description

NHI chromosomes map

[24399037.27%3A25202770.11]&zoom=10

Human Chromosomes frequencies.

ftp web site

The files downloaded contain: Gene name, Chromosomal position, AC, Swiss-Prot Entry name, MIM code, Description and are well formatted for import in Excel specifying TAB separator as rule for import.

Use this link to see the Human chromosome original files download from Expasy

The file downloaded do not contain the protein sequence in amino acid that we contruct manually starting from the column "Swiss-Prot Entry name" and using a Perl Script.

Some proteins appear duplicated.

The script download the FLAT file for each protein and put them one after the other in one single file for the chromosome considered.

The sequence is used to calculate the relative frequency for each amino acid within the protein, within the chromosomes.

R is used to create the density charts, to make the Kruskal-Wallis analysis and the Wilcoxon rank sum test with continuity correction automatically for each chromosome in a structurated way.

The R script divides the resulting data in directory, one for each chromosome.

Aim

The distribution of the amino acids within the chromosomes is not random. Some chromosomes
produce more AA of a certain type, others have a different distribution.
Our target is to understend this different behavior and study the single amino acid distribution within the chromosome in order to compare it with the more general distribution on the same amino acid on the whole human proteins.

Data

Method

Results

Tools
Attachments
fileuserdate
9727_kruskal_test_EQ_alto.xlsvernone31/01/2013
9728_kruskal_test_EQ_basso.xlsvernone31/01/2013
All_human_protein_aminoacidA_random_Normal_density.pdfvernone11/01/2013
All_human_protein_aminoacid_A_density.pdfvernone11/01/2013
CONT_AMINO_ID_humchr01_uniprot_org_NO_DUPLICATI_2013_1_10_1234.txtvernone10/01/2013
CONT_AMINO_ID_humchr02_uniprot_org_NO_DUPLICATI_2013_1_10_12232.txtvernone10/01/2013
CONT_AMINO_ID_humchr03_uniprot_org_NO_DUPLICATI_2013_1_10_1220.txtvernone10/01/2013
CONT_AMINO_ID_humchr04_uniprot_org_NO_DUPLICATI_2013_1_10_12130.txtvernone10/01/2013
CONT_AMINO_ID_humchr05_uniprot_org_NO_DUPLICATI_2013_1_10_12052.txtvernone10/01/2013
CONT_AMINO_ID_humchr06_uniprot_org_NO_DUPLICATI_2013_1_10_115913.txtvernone10/01/2013
CONT_AMINO_ID_humchr07_uniprot_org_NO_DUPLICATI_2013_1_10_115844.txtvernone10/01/2013
CONT_AMINO_ID_humchr08_uniprot_org_NO_DUPLICATI_2013_1_10_115812.txtvernone10/01/2013
CONT_AMINO_ID_humchr09_uniprot_org_NO_DUPLICATI_2013_1_10_115745.txtvernone10/01/2013
CONT_AMINO_ID_humchr10_uniprot_org_NO_DUPLICATI_2013_1_10_115713.txtvernone10/01/2013
CONT_AMINO_ID_humchr11_uniprot_org_NO_DUPLICATI_2013_1_10_115641.txtvernone10/01/2013
CONT_AMINO_ID_humchr12_uniprot_org_NO_DUPLICATI_2013_1_10_11560.txtvernone10/01/2013
CONT_AMINO_ID_humchr13_uniprot_org_NO_DUPLICATI_2013_1_10_115532.txtvernone10/01/2013
CONT_AMINO_ID_humchr14_uniprot_org_NO_DUPLICATI_2013_1_10_115446.txtvernone10/01/2013
CONT_AMINO_ID_humchr15_uniprot_org_NO_DUPLICATI_2013_1_10_11543.txtvernone10/01/2013
CONT_AMINO_ID_humchr16_uniprot_org_NO_DUPLICATI_2013_1_10_11530.txtvernone10/01/2013
CONT_AMINO_ID_humchr17_uniprot_org_NO_DUPLICATI_2013_1_10_115226.txtvernone10/01/2013
CONT_AMINO_ID_humchr18_uniprot_org_NO_DUPLICATI_2013_1_10_115146.txtvernone10/01/2013
CONT_AMINO_ID_humchr19_uniprot_org_NO_DUPLICATI_2013_1_10_115041.txtvernone10/01/2013
CONT_AMINO_ID_humchr20_uniprot_org_NO_DUPLICATI_2013_1_10_11506.txtvernone10/01/2013
CONT_AMINO_ID_humchr21_uniprot_org_NO_DUPLICATI_2013_1_10_11492.txtvernone10/01/2013
CONT_AMINO_ID_humchr22_uniprot_org_NO_DUPLICATI_2013_1_10_114822.txtvernone10/01/2013
CONT_AMINO_ID_humchrx_uniprot_org_NO_DUPLICATI_2013_1_10_11473.txtvernone10/01/2013
CONT_AMINO_ID_humchry_uniprot_org_NO_DUPLICATI_2013_1_10_11463.txtvernone10/01/2013
Chromosome_versus_tot_pdf01.pdfvernone23/01/2013
Chromosome_versus_tot_pdf010.pdfvernone23/01/2013
Chromosome_versus_tot_pdf011.pdfvernone23/01/2013
Chromosome_versus_tot_pdf012.pdfvernone23/01/2013
Chromosome_versus_tot_pdf013.pdfvernone23/01/2013
Chromosome_versus_tot_pdf014.pdfvernone23/01/2013
Chromosome_versus_tot_pdf015.pdfvernone23/01/2013
Chromosome_versus_tot_pdf016.pdfvernone23/01/2013
Chromosome_versus_tot_pdf017.pdfvernone23/01/2013
Chromosome_versus_tot_pdf018.pdfvernone23/01/2013
Chromosome_versus_tot_pdf019.pdfvernone23/01/2013
Chromosome_versus_tot_pdf02.pdfvernone23/01/2013
Chromosome_versus_tot_pdf020.pdfvernone23/01/2013
Chromosome_versus_tot_pdf021.pdfvernone23/01/2013
Chromosome_versus_tot_pdf022.pdfvernone23/01/2013
Chromosome_versus_tot_pdf03.pdfvernone23/01/2013
Chromosome_versus_tot_pdf04.pdfvernone23/01/2013
Chromosome_versus_tot_pdf05.pdfvernone23/01/2013
Chromosome_versus_tot_pdf06.pdfvernone23/01/2013
Chromosome_versus_tot_pdf07.pdfvernone23/01/2013
Chromosome_versus_tot_pdf08.pdfvernone23/01/2013
Chromosome_versus_tot_pdf09.pdfvernone23/01/2013
Chromosome_versus_tot_pdfx.pdfvernone23/01/2013
Chromosome_versus_tot_pdfy.pdfvernone23/01/2013
Chromosomepdf01.pdfvernone23/01/2013
Chromosomepdf010.pdfvernone23/01/2013
Chromosomepdf011.pdfvernone23/01/2013
Chromosomepdf012.pdfvernone23/01/2013
Chromosomepdf013.pdfvernone23/01/2013
Chromosomepdf014.pdfvernone23/01/2013
Chromosomepdf015.pdfvernone23/01/2013
Chromosomepdf016.pdfvernone23/01/2013
Chromosomepdf017.pdfvernone23/01/2013
Chromosomepdf018.pdfvernone23/01/2013
Chromosomepdf019.pdfvernone23/01/2013
Chromosomepdf02.pdfvernone23/01/2013
Chromosomepdf020.pdfvernone23/01/2013
Chromosomepdf021.pdfvernone23/01/2013
Chromosomepdf022.pdfvernone23/01/2013
Chromosomepdf03.pdfvernone23/01/2013
Chromosomepdf04.pdfvernone23/01/2013
Chromosomepdf05.pdfvernone23/01/2013
Chromosomepdf06.pdfvernone23/01/2013
Chromosomepdf07.pdfvernone23/01/2013
Chromosomepdf08.pdfvernone23/01/2013
Chromosomepdf09.pdfvernone23/01/2013
Chromosomepdfx.pdfvernone23/01/2013
Chromosomepdfy.pdfvernone23/01/2013
EQ_Glutammato_su_glutammina_basso_gruppi_diversi.xlsvernone24/01/2013
Human_protein_EQ_alto_densities.pdfvernone25/01/2013
Human_protein_EQ_alto_densityAAonEQ_versus_densityAAonTotal.pdfvernone25/01/2013
Human_protein_EQ_basso_densities.pdfvernone25/01/2013
Human_protein_EQ_basso_densityAAonEQ_versus_densityAAonTotal.pdfvernone25/01/2013
Human_protein_amino_acids_densities.pdfvernone22/01/2013
ID_humchr01_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr01_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr02_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr02_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr03_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr03_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr04_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr04_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr05_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr05_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr06_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr06_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr07_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr07_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr08_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr08_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr09_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr09_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr10_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr10_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr11_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr11_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr12_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr12_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr13_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr13_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr14_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr14_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr15_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr15_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr16_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr16_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr17_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr17_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr18_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr18_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr19_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr19_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr20_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr20_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr21_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr21_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchr22_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchr22_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchrx_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchrx_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
ID_humchry_uniprot_org_NO_DUPLICATI.txtvernone09/01/2013
ID_humchry_uniprot_org_NO_DUPLICATI.txt_FLAT.txtvernone09/01/2013
KLdiv_amino_TOT_versus_amino_TOT_random.txtvernone17/01/2013
KLdiv_amino_chromosome_versus_amino_chromosome_random.txtvernone18/01/2013
Mean_Human_ordinamento_standard.xlsvernone24/09/2013
humchr01_uniprot_org.xlsvernone08/01/2013
humchr02_uniprot_org.xlsvernone08/01/2013
humchr03_uniprot_org.xlsvernone08/01/2013
humchr04_uniprot_org.xlsvernone08/01/2013
humchr05_uniprot_org.xlsvernone08/01/2013
humchr06_uniprot_org.xlsvernone08/01/2013
humchr07_uniprot_org.xlsvernone08/01/2013
humchr08_uniprot_org.xlsvernone08/01/2013
humchr09_uniprot_org.xlsvernone08/01/2013
humchr10_uniprot_org.xlsvernone08/01/2013
humchr11_uniprot_org.xlsvernone08/01/2013
humchr12_uniprot_org.xlsvernone08/01/2013
humchr13_uniprot_org.xlsvernone08/01/2013
humchr14_uniprot_org.xlsvernone08/01/2013
humchr15_uniprot_org.xlsvernone08/01/2013
humchr16_uniprot_org.xlsvernone08/01/2013
humchr17_uniprot_org.xlsvernone08/01/2013
humchr18_uniprot_org.xlsvernone08/01/2013
humchr19_uniprot_org.xlsvernone08/01/2013
humchr20_uniprot_org.xlsvernone08/01/2013
humchr21_uniprot_org.xlsvernone08/01/2013
humchr21_uniprot_org_freq_rel_descrizioni_e_ID.xlsvernone18/06/2013
humchr22_uniprot_org.xlsvernone08/01/2013
humchrx_uniprot_org.xlsvernone08/01/2013
humchrx_uniprot_org_freq_rel_descrizioni_e_ID.xlsvernone18/06/2013
humchry_uniprot_org.xlsvernone08/01/2013
humchry_uniprot_org_freq_rel_descrizioni_e_ID.xlsvernone18/06/2013
kruscal_amino_chromosome_versus_amino_Human_TOT_su_valori_freqrel.csvvernone21/01/2013
kruscal_amino_chromosome_versus_amino_Human_TOT_su_valori_freqrel_analisi.xlsvernone23/01/2013
kruscal_amino_chromosome_versus_amino_Human_TOT_su_valori_freqrel_analisi_pvaluecorretto.xlsvernone25/01/2013
kruskal_test_EQ_alto.txtvernone25/01/2013
kruskal_test_EQ_alto.xlsvernone31/01/2013
kruskal_test_EQ_basso.txtvernone25/01/2013
kruskal_test_EQ_basso.xlsvernone31/01/2013
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