Notebook

OA Oyster Proteome Data VeriCheck¶

Supplemental file check¶

2fold and uniques

5folds

5fold

In [ ]:

SP / GO Annoation¶

http://eagle.fish.washington.edu/oyster/proteomics/supplemental%20data/Supp%20Data%20protein%20annotations.xlsx

erract "

SKYLINE DATA Check¶

uploaded raw to SQLSHare

Query

Still has duplicate peptides

Select PeptideSequence,
  count(*) as cnt
from [sr320@washington.edu].[OAMS_Skyline_p2_c_]
GROUP BY [PeptideSequence]
HAVING COUNT (*) > 2

Emma's Data

Query to verify

Select Count (*) 
  from
(
SELECT PeptideSequence,
  Count (*) as cnt 
  FROM 
  [emmats@washington.edu].[pep peak areas all oysters2.txt]
Group by PeptideSequence
  Having Count (*) > 1
)
go

In [2]:

!blastp -query /Volumes/web/cnidarian/OAMS_skyline_pep.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26\+/db/oyster_v9_aa -outfmt 6 -max_target_seqs 1 -out /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9.txt

Warning: lcl|Query_1 ID: Warning: One or more U or O characters replaced by X for alignment score calculations at positions 10

In [4]:

!head /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9.txt

1	CGI_10010163	100.00	14	0	0	1	14	108	121	0.010	30.8
2	CGI_10003288	100.00	10	0	0	1	10	228	237	1.0	24.6
3	CGI_10015115	100.00	10	0	0	1	10	762	771	0.62	25.4
4	CGI_10007640	100.00	10	0	0	1	10	1144	1153	1.0	25.0
5	CGI_10018366	100.00	10	0	0	1	10	106	115	1.6	23.9
6	CGI_10000265	100.00	24	0	0	1	24	134	157	7e-11	52.8
7	CGI_10014468	100.00	11	0	0	1	11	1027	1037	0.49	25.8
8	CGI_10014915	100.00	17	0	0	1	17	579	595	6e-06	40.8
9	CGI_10022396	100.00	10	0	0	1	10	315	324	0.36	26.2
10	CGI_10001357	100.00	10	0	0	1	10	241	250	0.034	29.3

In [5]:

!wc /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9.txt

   13078  156936  724094 /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9.txt

In [3]:

!blastp -query /Volumes/web/cnidarian/OAMS_skyline_pep.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26\+/db/oyster_v9_aa -outfmt 6 -max_target_seqs 4 -out /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9_b.txt

Warning: lcl|Query_1 ID: Warning: One or more U or O characters replaced by X for alignment score calculations at positions 10

In [7]:

!tail /Volumes/web/cnidarian/OAMS_skyline_Blastp_oysterb9_b.txt

14610	CGI_10003195	70.59	17	5	0	1	17	768	784	0.60	26.2
14610	CGI_10001323	70.59	17	5	0	1	17	143	159	0.41	26.6
14610	CGI_10018755	70.59	17	5	0	1	17	659	675	0.49	26.2
14610	CGI_10013230	70.59	17	5	0	1	17	1007	1023	0.52	26.2
14611	CGI_10003521	100.00	17	0	0	1	17	390	406	2e-05	39.7
14611	CGI_10003521	57.14	14	6	0	3	16	1468	1481	4.3	23.5
14611	CGI_10003521	53.85	13	6	0	4	16	606	618	9.2	22.3
14611	CGI_10008439	41.18	17	10	0	1	17	1105	1121	8.9	22.3
14612	CGI_10017178	100.00	17	0	0	1	17	458	474	1e-06	43.1
14612	CGI_10001407	100.00	17	0	0	1	17	385	401	1e-06	42.7

DE Proteins¶

http://eagle.fish.washington.edu/oyster/proteomics/supplemental%20data/Supp%20Data%20sig%20qvalue%20proteins2.txt

In [8]:

!head /Volumes/web/oyster/proteomics/supplemental\ data/Supp\ Data\ sig\ qvalue\ proteins2.txt

Treatment comparison	Protein	Fold change under stress	p-value	q-value	SwissProt Accession	BLASTx e-value	SwissProt Annotation
400 vs. 2800 µatm	CGI_10000591	0.68	0.0036	0.19	Q71LX4	1.00E-77	Talin-2
400 vs. 2800 µatm	CGI_10001585	2.42	0.0023	0.16	Q9W0E8	4.00E-126	Protein zer-1 homolog
400 vs. 2800 µatm	CGI_10002289	0.51	0.0041	0.19	Q9Y490	3.00E-76	Talin-1
400 vs. 2800 µatm	CGI_10002361	0.34	0.0015	0.16	P08011	1.00E-39	Microsomal glutathione S-transferase 1
400 vs. 2800 µatm	CGI_10003022	0.56	0.0066	0.20	Q9VN14	7.00E-13	Contactin
400 vs. 2800 µatm	CGI_10003145	0.56	0.0053	0.20	Q8NDM7	0	WD repeat-containing protein 96
400 vs. 2800 µatm	CGI_10003812	0.44	0.0021	0.16	Q32NR4	5.00E-94	Tetratricopeptide repeat protein 29
400 vs. 2800 µatm	CGI_10003897	0.74	0.0042	0.19	P18652	0	Ribosomal protein S6 kinase 2 alpha
400 vs. 2800 µatm	CGI_10003914	0.67	0.0058	0.20	Q9Y490	2.00E-177	Talin-1

IPath¶

http://eagle.fish.washington.edu/oyster/proteomics/supplemental%20data/Supp%20Data%20CGI_KEGG_association.txt

In [6]:

#probably not going to work with %
!head /Volumes/web/oyster/proteomics/supplemental\ data/Supp\ Data\ CGI_KEGG_association.txt

CGI_10028931	hsa:54847	0	642

Peptides¶

In [4]:

from pandas import *

# read data from data file into a pandas DataFrame  
oams_in = read_csv("/Users/sr320/Desktop/Supp Data Skyline output.csv") # name of the data file
            #sep="\t", # what character separates each column?
            #na_values=["", " ",]) # what values should be considered "blank" values?
        

In [5]:

print oams_in

<class 'pandas.core.frame.DataFrame'>
Int64Index: 50904 entries, 0 to 50903
Columns: 103 entries, ProteinName to 8_03 BestRetentionTime
dtypes: float64(2), int64(48), object(53)

In [6]:

oams_in.head()

Out[6]:

<class 'pandas.core.frame.DataFrame'>
Int64Index: 5 entries, 0 to 4
Columns: 103 entries, ProteinName to 8_03 BestRetentionTime
dtypes: float64(2), int64(48), object(53)

In [7]:

oams_in.count()

Out[7]:

ProteinName                50904
PeptideSequence            50904
PrecursorCharge            50904
PrecursorMz                50904
ProductCharge              50904
ProductMz                  50904
FragmentIon                50904
11_01 TotalArea            50904
11_01 BestRetentionTime    50904
11_02 TotalArea            50904
11_02 BestRetentionTime    50904
11_03 TotalArea            50904
11_03 BestRetentionTime    50904
2_01 TotalArea             50904
2_01 BestRetentionTime     50904
...
35_02 BestRetentionTime    50904
35_03 TotalArea            50904
35_03 BestRetentionTime    50904
5_01 TotalArea             50904
5_01 BestRetentionTime     50904
5_02 TotalArea             50904
5_02 BestRetentionTime     50904
5_03 TotalArea             50904
5_03 BestRetentionTime     50904
8_01 TotalArea             50904
8_01 BestRetentionTime     50904
8_02 TotalArea             50904
8_02 BestRetentionTime     50904
8_03 TotalArea             50904
8_03 BestRetentionTime     50904
Length: 103, dtype: int64

In [37]:

oams3.sum()

Out[37]:

protein    CGI_10000013CGI_10000033CGI_10000045CGI_100000...
CG2                                             1.460698e+11
CG5                                             1.069723e+11
CG8                                              9.31888e+10
CG11                                            1.052842e+11
CG26                                            1.281632e+11
CG29                                             7.01565e+10
CG32                                            5.606221e+10
CG35                                            8.597555e+10
CG221                                           1.472379e+11
CG224                                           1.213833e+11
CG227                                           1.531762e+11
CG230                                           9.807976e+10
CG242                                           7.674892e+10
CG245                                           1.392999e+11
CG248                                           1.274987e+11
CG251                                           1.218495e+11

In [38]:

oams3.mean()

Out[38]:

CG2      54564747.455610
CG5      39959762.291869
CG8      34810907.746420
CG11     39329175.735815
CG26     47875685.008945
CG29     26207134.783028
CG32     20942177.548209
CG35     32116380.094820
CG221    55001079.517204
CG224    45343045.513655
CG227    57219348.992819
CG230    36637939.460258
CG242    28669748.334060
CG245    52035818.414249
CG248    47627464.703441
CG251    45517176.820778

In [39]:

oams3.dropna()

Out[39]:

<class 'pandas.core.frame.DataFrame'>
Int64Index: 2677 entries, 0 to 3379
Data columns:
protein    2677  non-null values
CG2        2677  non-null values
CG5        2677  non-null values
CG8        2677  non-null values
CG11       2677  non-null values
CG26       2677  non-null values
CG29       2677  non-null values
CG32       2677  non-null values
CG35       2677  non-null values
CG221      2677  non-null values
CG224      2677  non-null values
CG227      2677  non-null values
CG230      2677  non-null values
CG242      2677  non-null values
CG245      2677  non-null values
CG248      2677  non-null values
CG251      2677  non-null values
dtypes: float64(16), object(1)

Spectral Count Method¶

In [ ]:

48 files that look like.... .   

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/SQLShare_-_View_Query_17B02CD9.png" alt="SQLShare_-_View_Query_17B02CD9.png"/>

Oysters 2-11 correspond to the 2800 µatm pCO2 treatment, 26-35 are 2800 µatm + mechanical stress, 221-230 are 400 µatm pCO2, and 242-251 are 400 µatm + mechanical stress.

In [20]:

!fetchdata.py -d ([emmats@washington.edu].[CG2 unique peps > 1]) -f tsv -o /Volumes/web/cnidarian/OA_.txt

/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `fetchdata.py -d ([emmats@washington.edu].[CG2 unique peps > 1]) -f tsv -o /Volumes/web/cnidarian/OA_.txt'

In [48]:

!fetchdata.py -d "[emmats@washington.edu].[CG251 unique peps >1]" -f tsv -o /Volumes/web/cnidarian/OA_MS_CG_251_upep.txt

In [35]:

!head /Volumes/web/cnidarian/OA_MS_CG_11_upep.txt

In [49]:

!fetchdata.py -d "[emmats@washington.edu].[NSAF all oysters]" -f tsv -o /Volumes/web/cnidarian/OA_MS_NSAFall.txt

In [50]:

!head /Volumes/web/cnidarian/OA_MS_NSAFall.txt

Spectral Count data 080813¶

CG2-11 = 2800 µatm 26-35 = 2800 + mech stress 221-230 = 400 µatm 242-251 = 400 + mech stress

In [1]:

!head /Users/sr320/Desktop/NSAF\ avg\ SpC.csv

CGI_10028023,0.00126516,0.000769597,0.001270981,0,0,0.001045932,0.001660575,0,0.001526871,0,0,0,0.001903786,0,0,0

#what to do.... Lets join in SQLShare, Group by GO slim, and do simple plot comparing individual in OA versus control....... then maybe mechanical versus non.

DAVID Enrichment Analysis¶

Comparing OA¶

In [2]:

#Supplemental file 4
!head /Volumes/web/oyster/proteomics/supplemental\ data/Supplementary\ Table\ S4.txt

CGI_10028902	0	0.00070663	0	0.000587183	0	0	0	0	0	0	0	0.000492864	0.000624293	0	0	0.000825286	0.000323453	0	0.000123216	0.000362395	2.625091303	2.941133862	0			*

SPIDs from the OA 5-fold column

P46778 P95896 Q9Y490 Q13247 Q6DF67 P74148 Q6V0I7 Q5XH14 Q9D1E6 O15484 Q08257 Q5ZLT7 Q8TD57 A6YLM6 Q64012 O75923 Q9Y6F1 Q6SP97 Q01989 Q3SZJ4 O02485 Q8BMF3 O97788 P49614 Q52KI8 Q9NQP4 P47727 Q60787 Q94887 Q7ZUG0 O00422 Q2PZL6 P61270 Q6IFY7 C3YWU0 P58365 P46781 O34355 D3YXS5 P31029 P55008 P46531 P06603 Q8R059 O42123 Q9DC69 A0QZA1 P34121 Q2NKZ1 P61958 Q9YI36 Q95V84 P19536 Q9UBV8 Q8NBX0 O35344 P56399 Q91YN5 Q8CGF7 P11584 Q2KJJ0 O09131 Q3SYW6 Q4R8N7 Q9WUA2 Q80W54 Q709C8 Q7Z3E1 Q5F408 P09324 Q16974 P51610 P91929 Q9LJN4 Q9VN14 P22817 B0BNA5 O00487 Q8WWI5 Q9Y2V2 Q922D8 P98158 Q92616 Q62638 Q6P5L8 Q8TC05 Q6TH15 Q5XIH7 A1ZA47 Q63ZH8 A2VEI2 Q15746 Q5XIG6 Q3SZ63 Q8AVS8 P19971

In [42]:

#file
!head /Volumes/web/cnidarian/chart_B1049AF0BD891379525818063.txt

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	4	4.49438202247191	0.003215314108718092	Q01989, Q94887, Q9Y490, Q9VN14	70	5	959	10.96	0.9080385953446322	0.9080385953446322	4.7758884843944305
GOTERM_BP_FAT	GO:0034330~cell junction organization	4	4.49438202247191	0.006099557106516472	Q01989, Q94887, Q9Y490, Q9VN14	70	6	959	9.133333333333333	0.9892581980951891	0.8963573354992699	8.877881028273594
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.3707865168539324	0.02785621995858589	Q94887, Q9Y490, Q9VN14	70	4	959	10.275	0.9999999991903415	0.9990679612912189	34.903309791067706
GOTERM_BP_FAT	GO:0048729~tissue morphogenesis	5	5.617977528089887	0.03480063151772505	Q01989, P46531, Q94887, Q5XIH7, P11584	70	18	959	3.805555555555555	0.9999999999960077	0.9985864712773175	41.62214279701073
GOTERM_BP_FAT	GO:0034329~cell junction assembly	3	3.3707865168539324	0.04428349052518013	Q94887, Q9Y490, Q9VN14	70	5	959	8.22	0.9999999999999973	0.9987844554464399	49.755240844743675
GOTERM_BP_FAT	GO:0060429~epithelium development	5	5.617977528089887	0.057813930529541334	Q01989, Q94887, Q9VN14, Q5XIH7, P11584	70	21	959	3.2619047619047614	1.0	0.9993604421596898	59.54296565749193
GOTERM_BP_FAT	GO:0010001~glial cell differentiation	3	3.3707865168539324	0.06337545723447832	P46531, Q94887, Q9VN14	70	6	959	6.85	1.0	0.9990227433649204	63.02363443000699
GOTERM_BP_FAT	GO:0048514~blood vessel morphogenesis	3	3.3707865168539324	0.06337545723447832	P46531, Q7Z3E1, P19971	70	6	959	6.85	1.0	0.9990227433649204	63.02363443000699
GOTERM_BP_FAT	GO:0048598~embryonic morphogenesis	5	5.617977528089887	0.06693586709090873	Q01989, P46531, Q94887, P58365, P11584	70	22	959	3.1136363636363633	1.0	0.9983667515177859	65.1028231919163

In [5]:

from IPython.display import YouTubeVideo
YouTubeVideo('3ZnhGLGVjk')

Out[5]:

In [43]:

!perl /Volumes/web/cnidarian/david_excelfix.pl /Volumes/web/cnidarian/chart_B1049AF0BD891379525818063.txt > /Volumes/web/cnidarian/mod_chart_B1049AF0BD891379525818063.txt

In [44]:

!head /Volumes/web/cnidarian/mod_chart_B1049AF0BD891379525818063.txt

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	4	4.49438202247191	0.003215314108718092	Q01989	70	5	959	10.96	0.9080385953446322	0.9080385953446322	4.7758884843944305
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	4	4.49438202247191	0.003215314108718092	 Q94887	70	5	959	10.96	0.9080385953446322	0.9080385953446322	4.7758884843944305
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	4	4.49438202247191	0.003215314108718092	 Q9Y490	70	5	959	10.96	0.9080385953446322	0.9080385953446322	4.7758884843944305
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	4	4.49438202247191	0.003215314108718092	 Q9VN14	70	5	959	10.96	0.9080385953446322	0.9080385953446322	4.7758884843944305
GOTERM_BP_FAT	GO:0034330~cell junction organization	4	4.49438202247191	0.006099557106516472	Q01989	70	6	959	9.133333333333333	0.9892581980951891	0.8963573354992699	8.877881028273594
GOTERM_BP_FAT	GO:0034330~cell junction organization	4	4.49438202247191	0.006099557106516472	 Q94887	70	6	959	9.133333333333333	0.9892581980951891	0.8963573354992699	8.877881028273594
GOTERM_BP_FAT	GO:0034330~cell junction organization	4	4.49438202247191	0.006099557106516472	 Q9Y490	70	6	959	9.133333333333333	0.9892581980951891	0.8963573354992699	8.877881028273594
GOTERM_BP_FAT	GO:0034330~cell junction organization	4	4.49438202247191	0.006099557106516472	 Q9VN14	70	6	959	9.133333333333333	0.9892581980951891	0.8963573354992699	8.877881028273594
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.3707865168539324	0.02785621995858589	Q94887	70	4	959	10.275	0.9999999991903415	0.9990679612912189	34.903309791067706

In [ ]:

#join in SQLShare

In [45]:

!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d OA_enrich2 /Volumes/web/cnidarian/mod_chart_B1049AF0BD891379525818063.txt

processing chunk line 0 to 51 (0.00206899642944 s elapsed)
pushing /Volumes/web/cnidarian/mod_chart_B1049AF0BD891379525818063.txt...
parsing C8BE2D77...
finished OA_enrich2

In [46]:

!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[OA_enrich2]g left join [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]sp on g.Genes = sp.SPID" -o /Volumes/web/cnidarian/OA_enrich2_join_SPID.csv

In [47]:

!head /Volumes/web/cnidarian/OA_enrich2_join_SPID.csv

In [48]:

!head /Volumes/web/cnidarian/OA_enrich2_join_SPID_sig.csv

Category,Term,Count,%,PValue,Genes,List Total,Pop Hits,Pop Total,Fold Enrichment,Bonferroni,Benjamini,FDR,CGI_ID,SPID,evalue,Description
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9Y490,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10000332,Q9Y490,3.00E-38,Talin-1
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9Y490,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10002289,Q9Y490,6.00E-69,Talin-1
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9VN14,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10002691,Q9VN14,9.00E-56,Contactin
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9VN14,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10003022,Q9VN14,6.00E-13,Contactin
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9VN14,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10006138,Q9VN14,1.00E-145,Contactin
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9Y490,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10011964,Q9Y490,0,Talin-1
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9Y490,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10012794,Q9Y490,7.00E-37,Talin-1
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q01989,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10013678,Q01989,0,Myosin heavy chain 95F
GOTERM_BP_FAT,GO:0045216~cell-cell junction organization,4,4.494382022,0.003215314,Q9VN14,70,5,959,10.96,0.908038595,0.908038595,4.775888484,CGI_10014483,Q9VN14,3.00E-106,Contactin

http://eagle.fish.washington.edu/cnidarian/OA_enrich2_join_SPID_sig.xls

Comparing mechanical stress at 400uatm¶

SPID from supp table 4; 5fold at 40uatm P47835 Q964E3 Q4PM47 Q53G44 Q54G05 A6NMZ7 Q9YI36 Q95V84 Q8NBX0 P07943 O75689 P15800 Q3UMR5 Q9D1E6 P85831 P56399 Q91YN5 A2BFC9 O83041 Q91312 A7SLW1 Q80W54 Q9Y6F1 Q6SP97 Q9N2W7 Q709C8 C3ZAH2 Q504A5 Q01989 Q9VI75 Q3SZJ4 Q9U943 Q8NBH2 P62197 B2RU80 O75494 Q8BMF3 Q9BW91 Q9D8W5 Q9NFT7 P49614 P91929 Q9LJN4 P22817 P43332 Q9BMX5 Q8TBY9 Q3SZ63 Q60787 Q5I085 Q80U96 C1C524 Q94887 A7Z035 Q90YV5 A0QZA1 Q7ZUG0 O00422 Q6INN8 Q08E38 Q6P5L8 Q6PCR7 Q8TC05 Q9NFT7 P21265 Q29451 A6NIH7 C3YWU0 P58365 P46781 Q9CXP4 O34355 D3YXS5 O95394 P56812 Q3SZ63

No enriched processes

2800 mechanincal Stress¶

5fold 2800 mechanical P85831 Q9Y6F1 Q9U943 Q8NBH2 Q94887 Q90YV5 Q7ZUG0 Q6INN8 C3YWU0 P58365 D3YXS5 Q9BEA9 P46778 P61958 Q80XI3 Q96PE7 P34826 P07686 Q5YW75 Q9Y490 Q9CQ60 Q13247 P74148 Q6V0I7 P19536 Q8K0U4 Q791V5 O35344 Q91ZU6 Q99805 Q0II68 Q62077 Q8CGF7 Q08257 P49696 B3A0P5 Q9MYM4 Q5ZLT7 Q9ESB5 P0CB95 Q8TD57 Q64012 Q9H4K1 P53356 O75923 Q6QLW4 P98060 P11046 Q68LP1 A5PJ65 P77735 Q9V3J1 Q5F408 P62752 P54353 P09324 P25071 P08630 O97788 Q08BB2 P10155 A6QR56 Q9VFC8 A4FUD6 Q2T9X2 Q9Y5B8 Q8ISN9 Q9VN14 P22892 Q28F51 Q710D6 Q9C0G6 P46531 Q8WWI5 Q96A72 Q91W63 Q9Y2V2 Q922D8 Q8LGG8 P52430 O17320 Q642C0 P13280 P26232 P61270 Q5RBM1 Q8HZK2 Q6IFY7 Q5XIH7 A1ZA47 Q8CFD1 Q5XIG6 Q5F408 Q6DKB0 Q95NR9 P31029 P55008 P19971 P43166 P55210

In [3]:

!head /Volumes/web/cnidarian/chart_976F753C30211379944509986.txt

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.49438202247191	0.007169536737378732	Q9MYM4, P58365, P07686, P26232	74	6	959	8.63963963963964	0.9964256357671437	0.9964256357671437	10.428890558189362
GOTERM_BP_FAT	GO:0050885~neuromuscular process controlling balance	3	3.3707865168539324	0.031023648581194604	Q9MYM4, P58365, P07686	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.3707865168539324	0.031023648581194604	Q94887, Q9Y490, Q9VN14	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0048729~tissue morphogenesis	5	5.617977528089887	0.04175586476702081	Q9MYM4, P46531, Q94887, Q5XIH7, P08630	74	18	959	3.59984984984985	0.9999999999999969	0.9999853687865333	47.94517596118537
GOTERM_BP_FAT	GO:0008366~axon ensheathment	3	3.3707865168539324	0.0491782737898529	Q94887, Q9VN14, P07686	74	5	959	7.775675675675677	1.0	0.9999483704675248	53.786476584957185
GOTERM_BP_FAT	GO:0034329~cell junction assembly	3	3.3707865168539324	0.0491782737898529	Q94887, Q9Y490, Q9VN14	74	5	959	7.775675675675677	1.0	0.9999483704675248	53.786476584957185
GOTERM_BP_FAT	GO:0019228~regulation of action potential in neuron	3	3.3707865168539324	0.0491782737898529	Q94887, Q9VN14, P07686	74	5	959	7.775675675675677	1.0	0.9999483704675248	53.786476584957185
GOTERM_BP_FAT	GO:0001508~regulation of action potential	3	3.3707865168539324	0.0491782737898529	Q94887, Q9VN14, P07686	74	5	959	7.775675675675677	1.0	0.9999483704675248	53.786476584957185
GOTERM_BP_FAT	GO:0007272~ensheathment of neurons	3	3.3707865168539324	0.0491782737898529	Q94887, Q9VN14, P07686	74	5	959	7.775675675675677	1.0	0.9999483704675248	53.786476584957185

</Volumes/web/cnidarian/chart_976F753C30211379944509986.txt>

In [4]:

!perl /Volumes/web/cnidarian/david_excelfix.pl /Volumes/web/cnidarian/chart_976F753C30211379944509986.txt > /Volumes/web/cnidarian/mod_chart_976F753C30211379944509986.txt

In [5]:

!head /Volumes/web/cnidarian/mod_chart_976F753C30211379944509986.txt

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.49438202247191	0.007169536737378732	Q9MYM4	74	6	959	8.63963963963964	0.9964256357671437	0.9964256357671437	10.428890558189362
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.49438202247191	0.007169536737378732	 P58365	74	6	959	8.63963963963964	0.9964256357671437	0.9964256357671437	10.428890558189362
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.49438202247191	0.007169536737378732	 P07686	74	6	959	8.63963963963964	0.9964256357671437	0.9964256357671437	10.428890558189362
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.49438202247191	0.007169536737378732	 P26232	74	6	959	8.63963963963964	0.9964256357671437	0.9964256357671437	10.428890558189362
GOTERM_BP_FAT	GO:0050885~neuromuscular process controlling balance	3	3.3707865168539324	0.031023648581194604	Q9MYM4	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0050885~neuromuscular process controlling balance	3	3.3707865168539324	0.031023648581194604	 P58365	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0050885~neuromuscular process controlling balance	3	3.3707865168539324	0.031023648581194604	 P07686	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.3707865168539324	0.031023648581194604	Q94887	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.3707865168539324	0.031023648581194604	 Q9Y490	74	4	959	9.719594594594595	0.9999999999808037	0.999995618637879	38.269514414920444

In [6]:

!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d 2800m_enrich2 /Volumes/web/cnidarian/mod_chart_976F753C30211379944509986.txt

processing chunk line 0 to 66 (0.000998973846436 s elapsed)
pushing /Volumes/web/cnidarian/mod_chart_976F753C30211379944509986.txt...
parsing 8723DBCB...
finished 2800m_enrich2

In [7]:

!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[2800m_enrich2]g left join [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]sp on g.Genes = sp.SPID" -o /Volumes/web/cnidarian/2800m_enrich2_join_SPID.csv

In [8]:

!head /Volumes/web/cnidarian/2800m_enrich2_join_SPID.csv

.07 pvalue thrshold http://eagle.fish.washington.edu/cnidarian/2800m_enrich2_join_SPID_sig.xls

In [ ]:

Research
P07686
Q9MYM4
Q9VFC8
P13280
C3YWU0
Q9CQ60
P10155
Q5XIG6

In [10]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/P07686 width=700 height=350></iframe>')

Out[10]:

In [11]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/Q9MYM4 width=700 height=350></iframe>')

Out[11]:

In [12]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/Q9VFC8 width=700 height=350></iframe>')

Out[12]:

In [14]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/P13280 width=700 height=350></iframe>')

Out[14]:

In [15]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/C3YWU0 width=700 height=350></iframe>')

Out[15]:

In [16]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/Q9CQ60 width=700 height=350></iframe>')

Out[16]:

In [17]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/P10155 width=700 height=350></iframe>')

Out[17]:

In [18]:

from IPython.display import HTML
HTML('<iframe src=http://www.uniprot.org/uniprot/Q5XIG6 width=700 height=350></iframe>')

Out[18]:

redux lets add qvalue proteins not 5 fold into david P22695 Q00651¶

In [20]:

!head /Volumes/web/cnidarian/chart_307AE9BAF7BE1379947826112.txt

Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0050905~neuromuscular process	4	4.395604395604396	0.007745415012843447	Q9MYM4, P58365, P07686, P26232	76	6	959	8.412280701754385	0.9979488423930916	0.9979488423930916	11.243775404230384
GOTERM_BP_FAT	GO:0048598~embryonic morphogenesis	6	6.593406593406594	0.023480583159572355	P46531, Q94887, Q00651, P58365, P11046, P08630	76	22	959	3.441387559808612	0.9999999938908196	0.9999218387540135	30.544682816797387
GOTERM_BP_FAT	GO:0050885~neuromuscular process controlling balance	3	3.296703296703297	0.0326636560370076	Q9MYM4, P58365, P07686	76	4	959	9.463815789473683	0.999999999996691	0.9998509845372993	39.915842133228416
GOTERM_BP_FAT	GO:0007043~cell-cell junction assembly	3	3.296703296703297	0.0326636560370076	Q94887, Q9Y490, Q9VN14	76	4	959	9.463815789473683	0.999999999996691	0.9998509845372993	39.915842133228416
GOTERM_BP_FAT	GO:0048729~tissue morphogenesis	5	5.4945054945054945	0.04551929059176884	Q9MYM4, P46531, Q94887, Q5XIH7, P08630	76	18	959	3.505116959064327	0.9999999999999999	0.9999058838959778	51.063867887999635
GOTERM_BP_FAT	GO:0019228~regulation of action potential in neuron	3	3.296703296703297	0.05170410612678131	Q94887, Q9VN14, P07686	76	5	959	7.571052631578947	1.0	0.9997864674362187	55.708473599859396
GOTERM_BP_FAT	GO:0001508~regulation of action potential	3	3.296703296703297	0.05170410612678131	Q94887, Q9VN14, P07686	76	5	959	7.571052631578947	1.0	0.9997864674362187	55.708473599859396
GOTERM_BP_FAT	GO:0045216~cell-cell junction organization	3	3.296703296703297	0.05170410612678131	Q94887, Q9Y490, Q9VN14	76	5	959	7.571052631578947	1.0	0.9997864674362187	55.708473599859396
GOTERM_BP_FAT	GO:0007272~ensheathment of neurons	3	3.296703296703297	0.05170410612678131	Q94887, Q9VN14, P07686	76	5	959	7.571052631578947	1.0	0.9997864674362187	55.708473599859396

In [ ]:

!perl /Volumes/web/cnidarian/david_excelfix.pl /Volumes/web/cnidarian/chart_307AE9BAF7BE1379947826112.txt > /Volumes/web/cnidarian/mod_chart_307AE9BAF7BE1379947826112.txt

In [22]:

!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d 2800m_enrich3 /Volumes/web/cnidarian/mod_chart_307AE9BAF7BE1379947826112.txt

processing chunk line 0 to 86 (0.000899076461792 s elapsed)
pushing /Volumes/web/cnidarian/mod_chart_307AE9BAF7BE1379947826112.txt...
parsing 77722FAD...
finished 2800m_enrich3

In [23]:

!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[2800m_enrich3]g left join [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]sp on g.Genes = sp.SPID" -o /Volumes/web/cnidarian/2800m_enrich3_join_SPID.csv

In [24]:

!head /Volumes/web/cnidarian/2800m_enrich3_join_SPID.csv

In [ ]: