Closed jvwong closed 6 years ago
Can you post the cy session file
Possibly related: for the "Ras Pathway" the painter is ignoring the max altogether (e.g. MAPK9). This happens on two different cys files.
The problem with the ras pathway example is that MAPK9 isnt found in the network.
I guess thats another hidden issue, the data in the table should be greyed out if it is not found in the network.
i would have assumed (until now) that the expression data is a subset of the geneset.
Its not from my experience. Anyways I pushed a fix to the demo branch can you see if it works for the p21 pathway?
At least the labels will not exactly be the same, for example there is no node with exactly MAPK9 but there is MAPKAP MAP3K7CL
FYI from the BioPAX. Take home message is that the BioPAX/SIF/GMT is unlike the SBGN.
E.g. for ras pathway (panther):
In BioPAX/GMT: 'JNK' has bp:memberEntityReference for 'MAPK8', 'MAPK9' and 'MAPK10' In SBGN: displays only 'JNK'
...
<bp:ProteinReference rdf:ID="ProteinReference_62367ea39ff44b5cf2c4af19e2f38838">
<bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Jun kinase n-terminal kinase</bp:standardName>
<bp:xref rdf:resource="#UnificationXref_panther_pathway_component_P04572" />
<bp:memberEntityReference rdf:resource="http://identifiers.org/uniprot/P45984" />
<bp:memberEntityReference rdf:resource="http://identifiers.org/uniprot/P45983" />
<bp:memberEntityReference rdf:resource="http://identifiers.org/uniprot/P53779" />
<bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">JNK</bp:displayName>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">ENTITY_REFERENCE_ID_DESC=Ras Pathway.PROTEIN.GENERIC.JNK</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">ENTITY_REFERENCE_NOTES= Long Name: Jun kinase n-terminal kinase Synonym: JNK,SAPK,stress activated protein kinase Accession: P04572 </bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">ENTITY_REFERENCE_PROTEIN_TYPE=GENERIC</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://www.pantherdb.org/pathways/biopax/P04393#_JNK_PROTEIN</bp:comment>
</bp:ProteinReference>
...
<bp:ProteinReference rdf:about="http://identifiers.org/uniprot/P45984">
<bp:entityFeature rdf:resource="#ModificationFeature_586e504f8d66ec6a2e781ff7cfbb2321" />
<bp:entityFeature rdf:resource="#ModificationFeature_465ab9bc807d1568b905867f7280d7d9" />
<bp:entityFeature rdf:resource="#ModificationFeature_5d1dd246f225aa6a1453b48ad695af02" />
<bp:entityFeature rdf:resource="#ModificationFeature_3e507a999d704211debd5a0f7661d8d1" />
<bp:standardName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Mitogen-activated protein kinase 9</bp:standardName>
<bp:xref rdf:resource="#UnificationXref_uniprot_knowledgebase_P45984" />
<bp:xref rdf:resource="#RelationshipXref_hgnc_symbol_MAPK9_identity" />
<bp:organism rdf:resource="http://identifiers.org/taxonomy/9606" />
<bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MK09_HUMAN</bp:displayName>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">PRKM9</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">SAPK1a</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">2.7.11.24</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Stress-activated protein kinase JNK2</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">Stress-activated protein kinase 1a</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MAPK 9</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MAP kinase 9</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">c-Jun N-terminal kinase 2</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">JNK2</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MAPK9</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">SAPK1A</bp:name>
<bp:name rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">JNK-55</bp:name>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://www.phosphosite.org/phosphosite.owl#po_3552</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://pathwaycommons.org/pc2/ProteinReference_uniprotkb_P45984_identity</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://pathwaycommons.org/pc2/ProteinReference_dip_DIP-281N_identity</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED ProteinRef_MAPK9__10090</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/uniprot/J3KNK1</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://mirtarbase.mbc.nctu.edu.tw/#ref_5601</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">FUNCTION: Serine/threonine-protein kinase involved in variousprocesses such as cell proliferation, differentiation, migration,transformation and programmed cell death. Extracellular stimulisuch as proinflammatory cytokines or physical stress stimulate thestress-activated protein kinase/c-Jun N-terminal kinase (SAP/JNK)signaling pathway. In this cascade, two dual specificity kinasesMAP2K4/MKK4 and MAP2K7/MKK7 phosphorylate and activate MAPK9/JNK2.In turn, MAPK9/JNK2 phosphorylates a number of transcriptionfactors, primarily components of AP-1 such as JUN and ATF2 andthus regulates AP-1 transcriptional activity. In response tooxidative or ribotoxic stresses, inhibits rRNA synthesis byphosphorylating and inactivating the RNA polymerase 1-specifictranscription initiation factor RRN3. Promotes stressed cellapoptosis by phosphorylating key regulatory factors including TP53and YAP1. In T-cells, MAPK8 and MAPK9 are required for polarizeddifferentiation of T-helper cells into Th1 cells. Upon T-cellreceptor (TCR) stimulation, is activated by CARMA1, BCL10, MAP2K7and MAP3K7/TAK1 to regulate JUN protein levels. Plays an importantrole in the osmotic stress-induced epithelial tight-junctionsdisruption. When activated, promotes beta-catenin/CTNNB1degradation and inhibits the canonical Wnt signaling pathway.Participates also in neurite growth in spiral ganglion neurons.Phosphorylates the CLOCK-ARNTL/BMAL1 heterodimer and plays a rolein the regulation of the circadian clock (PubMed:22441692).{ECO:0000269|PubMed:22441692}.FUNCTION: MAPK9 isoforms display different binding patterns:alpha-1 and alpha-2 preferentially bind to JUN, whereas beta-1 andbeta-2 bind to ATF2. However, there is no correlation betweenbinding and phosphorylation, which is achieved at about the sameefficiency by all isoforms. JUNB is not a substrate for JNK2alpha-2, and JUND binds only weakly to it.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.COFACTOR:Name=Mg(2+); Xref=ChEBI:CHEBI:18420;Evidence={ECO:0000269|PubMed:11062067};ENZYME REGULATION: Activated by threonine and tyrosinephosphorylation by either of two dual specificity kinases, MAP2K4and MAP2K7. MAP2K4 shows a strong preference for Tyr-185 whileMAP2K7 phosphorylates Tyr-183 preferentially. Inhibited by dualspecificity phosphatases, such as DUSP1.SUBUNIT: Interacts with MECOM (By similarity). Interacts withDCLK2 (By similarity). Binds to at least four scaffoldingproteins, MAPK8IP1/JIP-1, MAPK8IP2/JIP-2, MAPK8IP3/JIP-3/JSAP1 andSPAG9/MAPK8IP4/JIP-4. These proteins also bind other components ofthe JNK signaling pathway (By similarity). Interacts with NFATC4(PubMed:17875713). Interacts with ATF7; the interaction does notphosphorylate ATF7 but acts as a docking site for ATF7-associatedpartners such as JUN (PubMed:10376527). Interacts with BCL10(PubMed:17189706). Interacts with CTNNB1 and GSK3B(PubMed:19675674). Interacts with MAPKBP1 (PubMed:28089251).{ECO:0000250|UniProtKB:P49186, ECO:0000250|UniProtKB:Q9WTU6,ECO:0000269|PubMed:10376527, ECO:0000269|PubMed:17189706,ECO:0000269|PubMed:17875713, ECO:0000269|PubMed:19675674,ECO:0000269|PubMed:28089251}.SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19675674}.Nucleus {ECO:0000269|PubMed:19675674}.ALTERNATIVE PRODUCTS:Event=Alternative splicing; Named isoforms=5;Name=Alpha-2;IsoId=P45984-1; Sequence=Displayed;Name=Alpha-1;IsoId=P45984-2; Sequence=VSP_004835;Name=Beta-1;IsoId=P45984-3; Sequence=VSP_004834, VSP_004835;Name=Beta-2;IsoId=P45984-4; Sequence=VSP_004834;Name=5;IsoId=P45984-5; Sequence=VSP_041908, VSP_041909;DOMAIN: The TXY motif contains the threonine and tyrosine residueswhose phosphorylation activates the MAP kinases.PTM: Dually phosphorylated on Thr-183 and Tyr-185 by MAP2K7 andMAP2K4, which activates the enzyme. Autophosphorylated in vitro.{ECO:0000269|PubMed:11062067}.SIMILARITY: Belongs to the protein kinase superfamily. CMGCSer/Thr protein kinase family. MAP kinase subfamily.{ECO:0000305}.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncologyand Haematology;URL="http://atlasgeneticsoncology.org/Genes/JNK2ID426.html";WEB RESOURCE: Name=NIEHS-SNPs;URL="http://egp.gs.washington.edu/data/mapk9/"; COPYRIGHT: UniProt Consortium (www.uniprot.org). Distributed under the Creative Commons Attribution-NoDerivs License.</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED ProteinRef_MAPK9__9606</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/uniprot.isoform/P45984-1</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://pathwaycommons.org/pc2/ProteinReference_HPRD_04206_identity</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED ProteinRef_MAPK9__40674</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://www.phosphosite.org/phosphosite.owl#po_1234</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://www.ctdbase.org/#ref_protein_gene_5601</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/ncbigene/5601</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/refseq/NP_002743</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://pathwaycommons.org/pc2/ProteinReference_dip_DIP-270N_identity</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">MK09_HUMAN Reviewed; 424 AA.</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/refseq/NP_620709</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/refseq/NP_620708</bp:comment>
<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://identifiers.org/refseq/NP_620707</bp:comment>
</bp:ProteinReference>
Also your demo branch has deviated from the dev branch there are a few differences that are fixed in the dev branch such as only having two decimal places, etc.
THis 18fc20f15d0513f93b89c0585fc02fa2b8a26dad commit is still showing the decimals.
Nevermind I was thinking the demo branch.
Cherry-picked the commits over, you should have all the changes from the dev branch now.
Looks good. I think we need @IgorRodchenkov in on the discussion of how to reconcile GMT representation with SBGN representation. This ras pathway is an extreme example whereby only one gene maps!
Thats a story for another time.
The gene with maximum magnitude fold change is used as the bounds of the color map but it doesn't get colored in the graph. See example: