Handling Synopsis Lists

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Contents

Current Handling / Status

The Synopsis list

For the moment, our Synopsis is hold as an excel list.

Structure of the synopsis (excel)

The synopsis consists of an excel-sheet with the following columns:

1
ID
a unique counter for every gene and headline
2
Pathway a number for the pathway the headline or gene in this row belongs to (actually 1-78)
3
LfdNr a counter within every pathway for every gene and sub-headline
4
Unigene The Unigene-ID of the gene in this row. 0 for Headlines and sub-headlines
5
Title The Name of the gene or headline
6
Symbol The HGNC symbol for the gene in this row. Empty for headlines
7
ChromLoc The chromosomal locus for the gene in this row. Empty for headlines
8
EnsEMBL Gene ID The ENSG... for the gene in this row. 0 for headlines


And here as an example some short parts of the synopsis:


ID Pathway LfdNr Unigene Title Symbol ChromLoc Ensembl Gene ID
1 1 1 0 Stem Cell differentiation (WNT,Notch,HOX,FOXO) 0
2 1 2 0 WNT 0
3 1 3 Hs.248164 wingless-type MMTV integration site family, member 1 WNT1 12q13 ENSG00000125084
4 1 4 Hs.567356 wingless-type MMTV integration site family member 2 WNT2 7q31 ENSG00000105989
5 1 5 Hs.258575 wingless-type MMTV integration site family, member 2B WNT2B 1p13 ENSG00000134245
6 1 6 Hs.445884 wingless-type MMTV integration site family, member 3 WNT3 17q21 ENSG00000108379
7 1 7 Hs.336930 wingless-type MMTV integration site family, member 3A NOC
8 1 8 Hs.25766 CDNA clone IMAGE:3690160 WNT4 01p36.23-p35.1 ENSG00000162552
9 1 9 Hs.152213 Transcribed locus, strongly similar to NP_003383.2 wingless-type MMTV integration site family, member 5A precursor WNT5A 03p21-p14 ENSG00000114251
10 1 10 Hs.306051 Wingless-type MMTV integration site family, member 5B WNT5B 12p13.3 ENSG00000111186
11 1 11 Hs.29764 wingless-type MMTV integration site family, member 6 WNT6 2q35 ENSG00000115596
12 1 12 Hs.72290 wingless-type MMTV integration site family, member 7A WNT7A 3p25 ENSG00000154764
13 1 13 Hs.591274 wingless-type MMTV integration site family, member 8A WNT8A 5q31 ENSG00000061492
14 1 14 Hs.421281 wingless-type MMTV integration site family, member 8B WNT8B 10q24 ENSG00000075290
15 1 15 Hs.149504 Wingless-type MMTV integration site family, member 9A WNT9A 1q42 ENSG00000143816
16 1 16 Hs.326420 wingless-type MMTV integration site family, member 9B WNT9B 17q21 ENSG00000158955
17 1 17 Hs.121540 wingless-type MMTV integration site family, member 10A WNT10A 2q35 ENSG00000135925
18 1 18 Hs.91985 wingless-type MMTV integration site family, member 10B WNT10B 12q13 ENSG00000169884
19 1 19 Hs.108219 wingless-type MMTV integration site family, member 11 WNT11 11q13.5 ENSG00000085741
20 1 20 Hs.272375 wingless-type MMTV integration site family, member 16 WNT16 7q31 ENSG00000002745
21 1 21 Hs.592145 WNT1 inducible signaling pathway protein 2 WISP2 20q12-q13.1 ENSG00000064205
22 1 22 Hs.558428 WNT1 inducible signaling pathway protein 3 WISP3 6q21 ENSG00000112761
23 1 23 0 Frizzled 0
24 1 24 Hs.94234 frizzled homolog 1 (Drosophila) FZD1 7q21 ENSG00000157240
25 1 25 Hs.142912 frizzled homolog 2 (Drosophila) FZD2 17q21.1 ENSG00000180340
26 1 26 Hs.40735 frizzled homolog 3 (Drosophila) FZD3 8p21 ENSG00000104290
27 1 27 Hs.591968 frizzled homolog 4 (Drosophila) FZD4 11q14.2 ENSG00000174804
28 1 28 frizzled homolog 5 (Drosophila) FZD5 ENSG00000163251
29 1 29 Hs.591863 frizzled homolog 6 (Drosophila) FZD6 8q22.3-q23.1 ENSG00000164930
30 1 30 Hs.173859 frizzled homolog 7 (Drosophila) FZD7 2q33 ENSG00000155760
31 1 31 Hs.302634 frizzled homolog 8 (Drosophila) FZD8 10p11.21 ENSG00000177283
32 1 32 Hs.534367 frizzled homolog 9 (Drosophila) FZD9 7q11.23 ENSG00000188763
33 1 33 Hs.31664 frizzled homolog 10 (Drosophila) FZD10 12q24.33 ENSG00000111432
34 1 34 Hs.437846 smoothened homolog (Drosophila) SMO 7q32.3 ENSG00000128602
35 1 35 0 Frizzled interacting with Wnt 0
36 1 36 Hs.213424 secreted frizzled-related protein 1 SFRP1 8p12-p11.1 ENSG00000104332
37 1 37 Hs.481022 secreted frizzled-related protein 2 SFRP2 4q31.3 ENSG00000145423
38 1 38 Hs.128453 Frizzled-related protein FRZB 2qter ENSG00000162998
39 1 39 Hs.416007 secreted frizzled-related protein 4 SFRP4 7p14.1 ENSG00000106483
40 1 40 Hs.279565 secreted frizzled-related protein 5 SFRP5 10q24.1 ENSG00000120057
41 1 41 Hs.558009 secreted and transmembrane 1 SECTM1 17q25 ENSG00000141574
42 1 42 0 LRPs 0
43 1 43 Hs.162757 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) LRP1 12q13-q14 ENSG00000123384
44 1 44 Hs.470117 low density lipoprotein-related protein 1B (deleted in tumors) LRP1B 2q21.2 ENSG00000168702
45 1 45 Hs.470538 low density lipoprotein-related protein 2 LRP2 2q24-q31 ENSG00000081479
46 1 46 Hs.515340 low density lipoprotein receptor-related protein 3 LRP3 19q13.11 ENSG00000130881
47 1 47 Hs.4930 Low density lipoprotein receptor-related protein 4 LRP4 11p11.2-p12 ENSG00000134569
48 1 48 Hs.6347 Low density lipoprotein receptor-related protein 5 LRP5 11q13.4 ENSG00000162337
49 1 49 Hs.584775 low density lipoprotein receptor-related protein 6 LRP6 12p11-p13 ENSG00000070018
50 1 50 Hs.576154 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor LRP8 1p34 ENSG00000157193
51 1 51 Hs.525232 low density lipoprotein receptor-related protein 10 LRP10 14q11.2 ENSG00000197324
52 1 52 Hs.511818 retinoic acid early transcript 1E RAET1E 6q25.1 ENSG00000164520
53 1 53 Hs.517868 leucine rich repeat containing 3B LRRC3B 3p24 ENSG00000179796
54 1 54 Hs.502814 LRP16 protein LRP16 11q11
55 1 55 Hs.558513 LRP2 binding protein LRP2BP 4q35.1 ENSG00000109771
994 2 1 0 EGF-signaling 0
995 2 2 Hs.419815 epidermal growth factor (beta-urogastrone) EGF 4q25 ENSG00000138798
996 2 3 Hs.170009 transforming growth factor, alpha TGFA 2p13 ENSG00000163235
997 2 4 Hs.488293 epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) EGFR 7p12 ENSG00000146648
998 2 5 Hs.446352 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) ERBB2 17q21.1 ENSG00000141736
999 2 6 Hs.270833 Amphiregulin (schwannoma-derived growth factor) AREG 4q13-q21 ENSG00000205595
1000 2 7 Hs.632601 amphiregulin (schwannoma-derived growth factor) /// similar to Amphiregulin precursor (AR) (Colorectum cell-derived growth factor) (CRDGF) AREG /// LOC653193 4q13-q21 /// 4q13.3
1001 2 8 Hs.632601 Similar to Amphiregulin precursor (AR) (Colorectum cell-derived growth factor) (CRDGF) LOC653193 4q13.3
1002 2 9 Hs.118681 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) ERBB3 12q13 ENSG00000065361
1003 2 10 Hs.115263 epiregulin EREG 4q13.3 ENSG00000124882
1004 2 11 Hs.390729 v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) ERBB4 2q33.3-q34 ENSG00000178568
1005 2 12 Hs.799 heparin-binding EGF-like growth factor HBEGF 5q23 ENSG00000113070
1006 2 13 Hs.591704 betacellulin BTC 4q13-q21 ENSG00000174808
1007 2 14 Hs.385870 teratocarcinoma-derived growth factor 1 /// teratocarcinoma-derived growth factor 3, pseudogene TDGF1 /// TDGF3 3p21.31 /// Xq22.3
1008 2 15 Hs.503733 similar to cryptic LOC653275 2q21.1
1009 2 16 Hs.567542 cripto, FRL-1, cryptic family 1 /// similar to cryptic CFC1 /// LOC653275 2q21.1
1010 2 17 Hs.453951 neuregulin 1 NRG1 8p21-p12 ENSG00000157168
1011 2 18 Hs.408515 neuregulin 2 NRG2 5q23-q33 ENSG00000158458
1012 2 19 Hs.125119 neuregulin 3 NRG3 10q22-q23 ENSG00000185737
1013 2 20 Hs.238914 neuregulin 4 NRG4 15q24.2 ENSG00000169752
1014 2 21 Hs.591335 CD164 molecule, sialomucin CD164 6q21 ENSG00000135535
1015 2 22 Hs.213289 low density lipoprotein receptor (familial hypercholesterolemia) LDLR 19p13.3 ENSG00000130164
1016 2 23 Hs.162757 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) LRP1 12q13-q14 ENSG00000123384
1017 2 24 Hs.470117 low density lipoprotein-related protein 1B (deleted in tumors) LRP1B 2q21.2 ENSG00000168702
1018 2 25 Hs.470538 low density lipoprotein-related protein 2 LRP2 2q24-q31 ENSG00000081479
1019 2 26 Hs.137572 rhomboid, veinlet-like 1 (Drosophila) RHBDL1 16p13.3 ENSG00000103269
1020 2 27 Hs.524626 Rhomboid, veinlet-like 2 (Drosophila) RHBDL2 1p34.3 ENSG00000158315
1021 2 28 Hs.515340 low density lipoprotein receptor-related protein 3 LRP3 19q13.11 ENSG00000130881
1022 2 29 Hs.591196 rhomboid, veinlet-like 3 (Drosophila) RHBDL3 17q11.2 ENSG00000141314
1023 2 30 Hs.268177 phospholipase C, gamma 1 /// copine family member IX PLCG1 /// CPNE9 20q12-q13.1 /// 3p25.3
1024 2 31 Hs.4930 Low density lipoprotein receptor-related protein 4 LRP4 11p11.2-p12 ENSG00000134569
1025 2 32 Hs.6347 Low density lipoprotein receptor-related protein 5 LRP5 11q13.4 ENSG00000162337
1026 2 33 Hs.413111 phospholipase C, gamma 2 (phosphatidylinositol-specific) PLCG2 16q24.1 ENSG00000197943
1027 2 34 Hs.584775 low density lipoprotein receptor-related protein 6 LRP6 12p11-p13 ENSG00000070018
1028 2 35 Hs.132225 Phosphoinositide-3-kinase, regulatory subunit 1 (p85 alpha) PIK3R1 5q13.1 ENSG00000145675
1029 2 36 Hs.371344 phosphoinositide-3-kinase, regulatory subunit 2 (p85 beta) PIK3R2 19q13.2-q13.4 ENSG00000105647
1030 2 37 Hs.576154 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor LRP8 1p34 ENSG00000157193
1031 2 38 Hs.433795 SHC (Src homology 2 domain containing) transforming protein 1 SHC1 1q21 ENSG00000160691
1032 2 39 Hs.30965 SHC (Src homology 2 domain containing) transforming protein 2 SHC2 19p13.3 ENSG00000129946
1033 2 40 Hs.525232 low density lipoprotein receptor-related protein 10 LRP10 14q11.2 ENSG00000197324
1034 2 41 Hs.137570 SHC (Src homology 2 domain containing) transforming protein 3 SHC3 9q22.1 ENSG00000148082
1035 2 42 Hs.368592 sortilin-related receptor, L(DLR class) A repeats-containing SORL1 11q23.2-q24.2 ENSG00000137642
1036 2 43 Hs.370422 very low density lipoprotein receptor VLDLR 9p24 ENSG00000147852
1037 2 44 Hs.591774 Erbb2 interacting protein ERBB2IP 5q12.3 ENSG00000112851
1038 2 45 Hs.463928 discs, large homolog 4 (Drosophila) DLG4 17p13.1 ENSG00000132535
1039 2 46 Hs.78824 tyrosine kinase with immunoglobulin-like and EGF-like domains 1 TIE1 1p34-p33 ENSG00000066056
1040 2 47 Hs.444356 growth factor receptor-bound protein 2 GRB2 17q24-q25 ENSG00000177885
1041 2 48 Hs.89640 TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal) TEK 9p21 ENSG00000120156
1042 2 49 Hs.234074 delta-notch-like EGF repeat-containing transmembrane DNER ENSG00000187957
1043 2 50 Hs.477693 NCK adaptor protein 1 NCK1 3q21 ENSG00000158092
1044 2 51 Hs.529244 NCK adaptor protein 2 NCK2 2q12 ENSG00000071051
1045 2 52 Hs.2375 egf-like module containing, mucin-like, hormone receptor-like 1 EMR1 19p13.3 ENSG00000174837
1046 2 53 Hs.531619 egf-like module containing, mucin-like, hormone receptor-like 2 EMR2 19p13.1 ENSG00000127507
1047 2 54 Hs.461896 CDNA FLJ38130 fis, clone D6OST2000464 CRK 17p13.3 ENSG00000167193
1048 2 55 Hs.295626 integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) ITGB1 10p11.2 ENSG00000150093
1049 2 56 Hs.71215 docking protein 2, 56kDa DOK2 8p21.3 ENSG00000147443
1050 2 57 Hs.466039 CD97 molecule CD97 19p13 ENSG00000123146
1051 2 58 Hs.553501 RAS p21 protein activator (GTPase activating protein) 1 RASA1 5q13.3 ENSG00000145715
1052 2 59 Hs.495473 Notch homolog 1, translocation-associated (Drosophila) NOTCH1 9q34.3 ENSG00000148400
1053 2 60 Hs.98445 RAS p21 protein activator 2 RASA2 3q22-q23 ENSG00000155903
1054 2 61 Hs.369188 RAS p21 protein activator 3 RASA3 13q34 ENSG00000185989
1055 2 62 Hs.487360 Notch homolog 2 (Drosophila) NOTCH2 1p13-p11 ENSG00000134250
1056 2 63 Hs.417549 Protein tyrosine phosphatase, non-receptor type 1 PTPN1 20q13.1-q13.2 ENSG00000196396
1057 2 64 Hs.8546 Notch homolog 3 (Drosophila) NOTCH3 19p13.2-p13.1 ENSG00000074181
1058 2 65 Hs.436100 Notch homolog 4 (Drosophila) NOTCH4 6p21.3 ENSG00000204301
1059 2 66 Hs.63489 protein tyrosine phosphatase, non-receptor type 6 PTPN6 12p13 ENSG00000111679
1060 2 67 Hs.195659 v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) SRC 20q12-q13 ENSG00000197122
1061 2 68 Hs.379912 delta-like 1 (Drosophila) DLL1 6q27 ENSG00000198719
1062 2 69 Hs.431048 v-abl Abelson murine leukemia viral oncogene homolog 1 ABL1 9q34.1 ENSG00000097007
1063 2 70 Hs.533717 delta-like 1 homolog (Drosophila) DLK1 14q32 ENSG00000185559
1064 2 71 Hs.127792 Delta-like 3 (Drosophila) DLL3 19q13 ENSG00000090932
1065 2 72 Hs.18676 sprouty homolog 2 (Drosophila) SPRY2 13q31.1 ENSG00000136158
1066 2 73 Hs.22140 cell cycle exit and neuronal differentiation 1 CEND1 11p15.5 ENSG00000184524
1067 2 74 Hs.381912 sprouty homolog 3 (Drosophila) SPRY3 ENSG00000168939
1068 2 75 Hs.82848 selectin L (lymphocyte adhesion molecule 1) SELL 1q23-q25 ENSG00000188404
1069 2 76 Hs.468505 neurexin 1 NRXN1 2p16.3
1070 2 77 Hs.323308 Sprouty homolog 4 (Drosophila) SPRY4 5q31.3 ENSG00000187678
1071 2 78 Hs.323308 sprouty homolog 4 (Drosophila) /// similar to sprouty homolog 4 (Drosophila) SPRY4 /// LOC653170 5q31.3
1072 2 79 Hs.323308 sprouty homolog 4 (Drosophila) /// sprouty homolog 4 (Drosophila) SPRY4 5q31.3 ENSG00000187678
1073 2 80 Hs.372938 neurexin 2 NRXN2 11q13 ENSG00000110076
1074 2 81 Hs.525781 Sprouty-related, EVH1 domain containing 1 SPRED1 15q14 ENSG00000166068
1075 2 82 Hs.368307 neurexin 3 NRXN3 14q31 ENSG00000021645
1076 2 83 Hs.518055 leucine-rich repeats and immunoglobulin-like domains 1 LRIG1 3p14 ENSG00000144749
1077 2 84 Hs.332708 fibulin 5 FBLN5 14q32.1 ENSG00000140092
1078 2 85 Hs.482730 EGF-like repeats and discoidin I-like domains 3 EDIL3 5q14 ENSG00000164176
1079 2 86 Hs.179704 meprin A, alpha (PABA peptide hydrolase) MEP1A 6p12-p11 ENSG00000112818
1080 2 87 Hs.1274 bone morphogenetic protein 1 BMP1 8p21 ENSG00000168487
1081 2 88 Hs.106513 tolloid-like 1 TLL1 4q32-q33 ENSG00000038295
1082 2 89 Hs.154296 tolloid-like 2 TLL2 10q23-q24 ENSG00000095587
1083 2 90 Hs.465407 neuropilin (NRP) and tolloid (TLL)-like 1 NETO1 18q22-q23 ENSG00000166342
1084 2 91 Hs.444046 neuropilin (NRP) and tolloid (TLL)-like 2 NETO2 16q11 ENSG00000171208
1085 2 92 Hs.177959 ADAM metallopeptidase domain 2 (fertilin beta) ADAM2 8p11.2 ENSG00000104755
1086 2 93 Hs.98848 ADAM metallopeptidase domain 3a (cyritestin 1) ADAM3A 8p21-p12
1087 2 94 Hs.97508 ADAM metallopeptidase domain 6 ADAM6 14q32.33
1088 2 95 Hs.116147 ADAM metallopeptidase domain 7 ADAM7 8p21.2 ENSG00000069206
1089 2 96 Hs.501574 ADAM metallopeptidase domain 8 /// ADAM metallopeptidase domain 8 ADAM8 10q26.3 ENSG00000151651



Problems

Because of the need of sharing the synopsis the biggest problem is getting a synchronised Synopsis back if more than people download the list, edit it, and upload it back to the server.
All the different versions will lead to a unmanageable mess.
For that reason, it is indispensable to change the handling for the synopsis.
Collaborating on an excel sheet leads to a mess.

Requirements to new system

  • moving genes or blocks of genes from one to an other pathway
  • Adding/Deleting/Moving pathways
  • Adding/Deleting/Moving subgroups of pathways
  • Adding more complex annotations to genes/pathways/pathwaysubgroups
  • Adding/Deleting/Moving genes. Whole blocks at once should be possible
  • Versioning
    • Every action has to logged with following information:
      WHO has done WHAT at WHAT TIME
    • Every action must be restoreable. (Like the history mechanism in Wiki)
  • Keep a defined order, change an order
  • For further analysis (like matching synopsis versus exeriments) excel is quite good.
    --> support a synopsis download as excel.
    In future, create online tools for matching.
  • user - rigths management --> use of Wiki - Account for login - required. (one account --> whole access)
  • Visulatisation of Synopsis should be done as a navigation tree.
    Check to example how it should look like: http://www.destroydrop.com/javascripts/tree/

Approaches

Approach Advantage Disadvantage
Using Lipidnet form ISB Many of the necessary functionalities are  available;

Covers most problems like adding, deleting; Already has the desired structure.

No Code available; no single login;

No automatic upload for batch files. Slowly, some bugs; dependent on ISB.

With Wiki Easy to edit; everyone has the same account; a batch of genes is easy to add; Difficult generating Excel files also importing Excel files -> writing parsers. Splitting of the whole list necessary; speed problems
With adapted “Verfahrensliste” A prototype can be rapidly made; easy export/import to/from Excel; Some changes necessary for single login; every functionality has to be programmed by ourselves;
With Excel files accessible via ftp-server Initial working with the files is very easy; Difficult to merge several version; no versions on dataset level only on file level
With Excel files with CVS Initial working with the files is very easy; Difficult to merge several versions; no versions on dataset level only on file level; every client needs a special client tortoise-cvs;
Googling for existing php-modules which implements a usable structure for displaying and working with the synopsis list


Conclusion: We make a prototype with the “Verfahrensliste” and decide then.

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