Quick start 1: How do I build OmniPath data with pypath?

pypath provides an easy way to build the OmniPath network as it has been described in our paper. At the first time this will take several minutes, because all data will be downloaded from the original providers. Next time pypath will use the data from its cache directory, so the network will build much faster. If you want to load it even faster, you can save it into a pickle dump.

In [ ]:

Quick start 2: I just want a network quickly and play around with pypath

You can find the predefined formats in the pypath.data_formats module. For example, to load one resource from there, let's say Signor:

In [ ]:

Or to load all process description resources:

In [ ]:

Quick start 3: How do I build networks from any data with pypath?

Here we show how to build a network from your own files. The advantage of building network with pypath is that you don't need to worry about merging redundant elements, neither about different formats and identifiers. Let's say you have two files with network data:

network1.csv

entrezA,entrezB,effect
1950,1956,inhibition
5290,207,stimulation
207,2932,inhibition
1956,5290,stimulation

network2.sif

EGF + EGFR
EGFR + PIK3CA
EGFR + SOS1
PIK3CA + RAC1
RAC1 + MAP3K1
SOS1 + HRAS
HRAS + MAP3K1
PIK3CA + AKT1
AKT1 - GSK3B

Note: you need to create these files in order to load them.

1: Defining input formats

In [1]:

2: Creating PyPath object and loading the 2 test files

In [2]:
	=== d i s c l a i m e r ===

	All data coming with this module
	either as redistributed copy or downloaded using the
	programmatic interfaces included in the present module
	are available under public domain, are free to use at
	least for academic research or education purposes.
	Please be aware of the licences of all the datasets
	you use in your analysis, and please give appropriate
	credits for the original sources when you publish your
	results. To find out more about data sources please
	look at `pypath.descriptions` and
	`pypath.data_formats.urls`.

	» New session started,
	session ID: 'g0p8r'
	logfile:'./log/g0p8r.log'.
	:: Loading data from cache previously downloaded from www.uniprot.org
	:: Ready. Resulted `plain text` of type file object. 
	:: Local file at `/home/denes/Dokumentumok/pw/dev/src/cache/ec920965677ac83b8805d72853c79d45-`.
	:: Loading data from cache previously downloaded from www.uniprot.org
	:: Ready. Resulted `plain text` of type file object. 
	:: Local file at `/home/denes/Dokumentumok/pw/dev/src/cache/ec920965677ac83b8805d72853c79d45-`.
	:: Loading data from cache previously downloaded from ftp.uniprot.org
	:: Ready. Resulted `gz extracted data` of type file object. 
	:: Local file at `/home/denes/Dokumentumok/pw/dev/src/cache/079410d8e3f429e7699c167b9d4ef3b7-HUMAN_9606_idmapping.dat.gz`.
	:: Processing ID conversion list: finished, 100.0% [0:00:06 elapsed]
 » egf2
	:: Loading 'genesymbol' to 'uniprot' mapping table
	:: Loading 'uniprot-sec' to 'uniprot-pri' mapping table
	:: Loading 'genesymbol' to 'trembl' mapping table
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » egf1
	:: Loading 'genesymbol' to 'swissprot' mapping table
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]

 :: Comparing with reference lists... done.

 » 9 interactions between 9 nodes
 from 2 resources have been loaded,
 for details see the log: ./log/g0p8r.log

3: Plotting the network with igraph

In [3]:
Out[3]:

4: Querying the PyPath object

This object offers many methods for analysing the network and also for integrating additional data. Let's see some examples. List those proteins stimulating the protein PIK3CA:

In [4]:
	:: Setting directions: finished, 100.0% [0:00:00 elapsed]
Out[4]:
['EGFR']

And those stimulated by PIK3CA:

In [5]:
Out[5]:
['AKT1', 'RAC1']

In the background in order to run these queries, pypath converted the network to a directed graph:

In [7]:
pa.graph is directed: False
pa.dgraph is directed: True

5: Loading more data

In [8]:
	:: Loading data from cache previously downloaded from www.uniprot.org
	:: Ready. Resulted `plain text` of type file object. 
	:: Local file at `/home/denes/Dokumentumok/pw/dev/src/cache/ec920965677ac83b8805d72853c79d45-`.
 » DeathDomain
	:: Reading from cache: cache/deathdomain.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » PDZBase
	:: Reading from cache: cache/pdzbase.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » Guide2Pharma
	:: Reading from cache: cache/guide2pharma.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » SignaLink3
	:: Reading from cache: cache/signalink3.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:01 elapsed]
 » CA1
	:: Reading from cache: cache/ca1.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » ARN
	:: Reading from cache: cache/arn.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » SPIKE
	:: Reading from cache: cache/spike.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:01 elapsed]
 » NRF2ome
	:: Reading from cache: cache/nrf2ome.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » TRIP
	:: Reading from cache: cache/trip.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]
 » Signor
	:: Reading from cache: cache/signor.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:03 elapsed]
 » Macrophage
	:: Reading from cache: cache/macrophage.edges.pickle
	:: Processing nodes: finished, 100.0% [0:00:00 elapsed]
	:: Processing edges: finished, 100.0% [0:00:00 elapsed]
	:: Processing attributes: finished, 100.0% [0:00:00 elapsed]

 :: Comparing with reference lists... done.

 » 13914 interactions between 4561 nodes
 from 13 resources have been loaded,
 for details see the log: ./log/g0p8r.log

6: Further attributes in the PyPath object

We just loaded pathway data from the pathway resources in OmniPath. The 2 small example networks are among the sources, the new ones have been added.

In [20]:
Out[20]:
['SignaLink3', 'SPIKE', 'egf2', 'Signor', 'egf1']

We can also see the directions and effects of this interaction:

In [21]:
Directions and signs of interaction between P00533 and P01133

	P00533 <=== P01133 :: SPIKE, SignaLink3, egf2, Signor, egf1
	P00533 ==== P01133 :: egf2, egf1
	P00533 <=+= P01133 :: SignaLink3, egf2, Signor, SPIKE
	P00533 <=-= P01133 :: egf1

As we see, the first example network wrongly had EGF inhibiting EGFR.

But what is gs()? It is a shorthand for genesymbol(), facilitating querying the object by human readable names. Let's see what other stimulators 'PIK3CA' has now based on all the resources above.

In [35]:
['EGFR', 'HRAS', 'IGF1R', 'ERBB4', 'ERBB2', 'NTRK1', 'PTPN11', 'IRS1', 'NRAS', 'KRAS', 'PIK3R3', 'GNGT1', 'GRB10', 'IRS2', 'GAB2', 'SRC', 'SHC1', 'TNF', 'ITGB4', 'GAB1', 'ERBB3', 'PIK3AP1', 'GNB1', 'GNG3', 'GNG2', 'GNG12', 'GNB3']

And its inhibitors:

In [28]:
Out[28]:
['CBLB', 'GNA11']

The gs_ in front means we query by GeneSymbol, this returns a special VertexSeq object:

In [29]:
Out[29]:
<pypath.main._NamedVertexSeq at 0x7f1a22b2e690>

It's possible to get generators to iterate this vertex sequence, for example by GeneSymbols:

In [30]:
Out[30]:
<generator object genesymbol at 0x7f1a1c25ba50>

Or by UniProt IDs:

In [31]:
Out[31]:
['Q13191', 'P29992']

Or by igraph.Vertex objects:

In [32]:
Out[32]:
[igraph.Vertex(<igraph.Graph object at 0x7f1a2573dde0>,673,{'g2p_receptor': False, 'nameType': 'uniprot', 'originalNames': {'Q13191': 'uniprot'}, 'name': 'Q13191', 'ncbi_tax_id': 9606, 'color': '#49969AAA', 'type': 'protein', 'ca1_location': 'Cytosol', 'label': 'CBLB', 'sources': ['SignaLink3', 'CA1', 'Signor'], 'references': [<pypath.input_formats.Reference object at 0x7f1a1cb57a10>, <pypath.input_formats.Reference object at 0x7f1a22f32750>, <pypath.input_formats.Reference object at 0x7f1a144cb950>, <pypath.input_formats.Reference object at 0x7f1a22f327d0>, <pypath.input_formats.Reference object at 0x7f1a14e8a910>, <pypath.input_formats.Reference object at 0x7f1a22f32650>, <pypath.input_formats.Reference object at 0x7f1a240112d0>, <pypath.input_formats.Reference object at 0x7f1a19ee0110>, <pypath.input_formats.Reference object at 0x7f1a185f6350>, <pypath.input_formats.Reference object at 0x7f1a22f32710>, <pypath.input_formats.Reference object at 0x7f1a1c6bd750>, <pypath.input_formats.Reference object at 0x7f1a24011350>, <pypath.input_formats.Reference object at 0x7f1a22f32610>], 'slk_pathways': ['IIP', 'BCR', 'RTK'], 'g2p_ligand': False, 'atg': u'', 'label_size': 6.461639649487954, 'label_color': '#007B7FFF', 'exp': None, 'ca1_function': 'Ubiquitinase'}),
 igraph.Vertex(<igraph.Graph object at 0x7f1a2573dde0>,1940,{'g2p_receptor': False, 'nameType': 'uniprot', 'originalNames': {'P29992': 'uniprot', u'GNA11': 'genesymbol'}, 'name': 'P29992', 'ncbi_tax_id': 9606, 'color': '#49969AAA', 'type': 'protein', 'ca1_location': 'Cytosol', 'label': 'GNA11', 'sources': ['SignaLink3', 'CA1', 'Signor', 'SPIKE'], 'references': [<pypath.input_formats.Reference object at 0x7f1a1850a590>, <pypath.input_formats.Reference object at 0x7f1a17106f90>, <pypath.input_formats.Reference object at 0x7f1a170af110>, <pypath.input_formats.Reference object at 0x7f1a14a45ad0>, <pypath.input_formats.Reference object at 0x7f1a170af5d0>, <pypath.input_formats.Reference object at 0x7f1a22f32510>, <pypath.input_formats.Reference object at 0x7f1a1c96e3d0>, <pypath.input_formats.Reference object at 0x7f1a22f37cd0>, <pypath.input_formats.Reference object at 0x7f1a22e1d910>, <pypath.input_formats.Reference object at 0x7f1a170af190>, <pypath.input_formats.Reference object at 0x7f1a22baa650>, <pypath.input_formats.Reference object at 0x7f1a2306fc50>], 'slk_pathways': ['GPCR', 'IIP'], 'g2p_ligand': False, 'atg': u'', 'label_size': 6.364690776650755, 'label_color': '#007B7FFF', 'exp': None, 'ca1_function': 'Gprotein'})]

affects and affected_by methods query the molecules affected by or having an effect on the target respectively, either stimulation, inhibition or unknown effect:

In [34]:
['SOS1', 'PIK3CA', 'ERBB2', 'ANXA1', 'STAT3', 'NCK1', 'CLTA', 'SHC2', 'VAV2', 'SFN', 'ALCAM', 'GRAP', 'PTPN11', 'CASP1', 'FOS', 'SLC3A2', 'ESR1', 'S100A7', 'CASP3', 'HOXC10', 'SHC3', 'PTK2', 'TUBA1A', 'CAV2', 'CAV1', 'ICAM1', 'GRB2', 'GAPDH', 'ATP1A1', 'ATP1B1', 'GSTP1', 'STAT5A', 'STAT1', 'LYN', 'CBL', 'ERRFI1', 'S100A9', 'CDH1', 'HGS', 'PIK3R1', 'PLCG1', 'JAK1', 'MAP2K1', 'CASP7', 'NCK2', 'E2F1', 'EZR', 'STAT5B', 'SHC1', 'PTPN1', 'CCND1', 'MUC1', 'SEC13', 'LRIG1', 'PTK2B', 'GAB1', 'SOCS5', 'ERBB3', 'CALM2', 'WASF1', 'PKIA', 'PRKDC', 'EPB41', 'RGS16', 'HDAC6', 'PCNA', 'TRPV3', 'EPS15', 'PIK3C2B']

Those proteins affecting EGFR; we see EGF among them:

In [36]:
['EGF', 'ERBB2', 'RARA', 'AREGB', 'STAT3', 'BTC', 'TLR2', 'PTPN2', 'SOCS4', 'VAV2', 'TP53', 'PKN1', 'PTPN11', 'CBLB', 'CASP1', 'MAPK1', 'ABL1', 'MAPK11', 'TLR4', 'AP2M1', 'CAV1', 'EGR1', 'STAT1', 'CDK1', 'PRKCA', 'CBL', 'ERRFI1', 'JAK1', 'MAPK3', 'TGFA', 'JAK2', 'SRC', 'HBEGF', 'SNX9', 'PTPN6', 'PTPN1', 'MUC1', 'RIN1', 'LRIG1', 'PTK2B', 'ITGB4', 'SOCS5', 'MAPK14', 'MMP2', 'JUNB', 'EREG', 'GPER1', 'EPN1', 'EPGN']

The direct neighbors, without being aware of the directions are retrieved by neighbors methods:

In [37]:
['SOS1', 'PIK3CA', 'EGF', 'ERBB4', 'ERBB2', 'ANXA1', 'RASA1', 'RARA', 'AREGB', 'STAT3', 'NCK1', 'BTC', 'CLTA', 'TLR2', 'PTPN2', 'SHC2', 'SOCS4', 'VAV2', 'TP53', 'PKN1', 'SFN', 'ALCAM', 'GRAP', 'PTPN11', 'CBLB', 'CASP1', 'MAPK1', 'FOS', 'SLC3A2', 'ESR1', 'S100A7', 'ABL1', 'CASP3', 'HOXC10', 'SHC3', 'PTK2', 'MAPK11', 'TLR4', 'TUBA1A', 'CAV2', 'AP2M1', 'CAV1', 'ICAM1', 'GRB2', 'EGR1', 'GAPDH', 'ATP1A1', 'ATP1B1', 'GSTP1', 'STAT5A', 'STAT1', 'LYN', 'CDK1', 'PRKCA', 'CBL', 'ERRFI1', 'S100A9', 'GRB7', 'CDH1', 'HGS', 'PIK3R1', 'PLCG1', 'JAK1', 'MAP2K1', 'MAPK3', 'TGFA', 'JAK2', 'SRC', 'HBEGF', 'CASP7', 'NCK2', 'E2F1', 'SNX9', 'EZR', 'STAT5B', 'SHC1', 'PTPN6', 'PTPN1', 'CCND1', 'MUC1', 'RIN1', 'SEC13', 'LRIG1', 'CRK', 'PTK2B', 'ITGB4', 'GAB1', 'SOCS5', 'MAPK14', 'ERBB3', 'CALM2', 'WASF1', 'PKIA', 'PRKDC', 'EPB41', 'MMP2', 'CBLC', 'RGS16', 'JUNB', 'HDAC6', 'PCNA', 'TRPV1', 'TRPV3', 'PKD2', 'EPS15', 'EREG', 'GPER1', 'PIK3C2B', 'EPN1', 'EPGN']

The neighborhood methods return the indirect neighborhood in custom number of steps (however size of the neighborhood increases rapidly with number of steps):

In [40]:
['EGFR', 'SOS1', 'PIK3CA', 'EGF', 'ERBB4', 'ERBB2', 'ANXA1', 'RASA1', 'RARA', 'AREGB', 'STAT3', 'NCK1', 'BTC', 'CLTA', 'TLR2', 'PTPN2', 'SHC2', 'SOCS4', 'VAV2', 'TP53', 'PKN1', 'SFN', 'ALCAM', 'GRAP', 'PTPN11', 'CBLB', 'CASP1', 'MAPK1', 'FOS', 'SLC3A2', 'ESR1', 'S100A7', 'ABL1', 'CASP3', 'HOXC10', 'SHC3', 'PTK2', 'MAPK11', 'TLR4', 'TUBA1A', 'CAV2', 'AP2M1', 'CAV1', 'ICAM1', 'GRB2', 'EGR1', 'GAPDH', 'ATP1A1', 'ATP1B1', 'GSTP1', 'STAT5A', 'STAT1', 'LYN', 'CDK1', 'PRKCA', 'CBL', 'ERRFI1', 'S100A9', 'GRB7', 'CDH1', 'HGS', 'PIK3R1', 'PLCG1', 'JAK1', 'MAP2K1', 'MAPK3', 'TGFA', 'JAK2', 'SRC', 'HBEGF', 'CASP7', 'NCK2', 'E2F1', 'SNX9', 'EZR', 'STAT5B', 'SHC1', 'PTPN6', 'PTPN1', 'CCND1', 'MUC1', 'RIN1', 'SEC13', 'LRIG1', 'CRK', 'PTK2B', 'ITGB4', 'GAB1', 'SOCS5', 'MAPK14', 'ERBB3', 'CALM2', 'WASF1', 'PKIA', 'PRKDC', 'EPB41', 'MMP2', 'CBLC', 'RGS16', 'JUNB', 'HDAC6', 'PCNA', 'TRPV1', 'TRPV3', 'PKD2', 'EPS15', 'EREG', 'GPER1', 'PIK3C2B', 'EPN1', 'EPGN']

['EGFR', 'SOS1', 'PIK3CA', 'EGF', 'ERBB4', 'ERBB2', 'ANXA1', 'RASA1', 'RARA', 'AREGB', 'STAT3', 'NCK1', 'BTC', 'CLTA', 'TLR2', 'PTPN2', 'SHC2', 'SOCS4', 'VAV2', 'TP53', 'PKN1', 'SFN', 'ALCAM', 'GRAP', 'PTPN11', 'CBLB', 'CASP1', 'MAPK1', 'FOS', 'SLC3A2', 'ESR1', 'S100A7', 'ABL1', 'CASP3', 'HOXC10', 'SHC3', 'PTK2', 'MAPK11', 'TLR4', 'TUBA1A', 'CAV2', 'AP2M1', 'CAV1', 'ICAM1', 'GRB2', 'EGR1', 'GAPDH', 'ATP1A1', 'ATP1B1', 'GSTP1', 'STAT5A', 'STAT1', 'LYN', 'CDK1', 'PRKCA', 'CBL', 'ERRFI1', 'S100A9', 'GRB7', 'CDH1', 'HGS', 'PIK3R1', 'PLCG1', 'JAK1', 'MAP2K1', 'MAPK3', 'TGFA', 'JAK2', 'SRC', 'HBEGF', 'CASP7', 'NCK2', 'E2F1', 'SNX9', 'EZR', 'STAT5B', 'SHC1', 'PTPN6', 'PTPN1', 'CCND1', 'MUC1', 'RIN1', 'SEC13', 'LRIG1', 'CRK', 'PTK2B', 'ITGB4', 'GAB1', 'SOCS5', 'MAPK14', 'ERBB3', 'CALM2', 'WASF1', 'PKIA', 'PRKDC', 'EPB41', 'MMP2', 'CBLC', 'RGS16', 'JUNB', 'HDAC6', 'PCNA', 'TRPV1', 'TRPV3', 'PKD2', 'EPS15', 'EREG', 'GPER1', 'PIK3C2B', 'EPN1', 'EPGN', 'HRAS', 'NRAS', 'KRAS', 'SPRY2', 'LCK', 'SPRY1', 'SPRY3', 'ITSN1', 'AKT1', 'RAC1', 'IGF1R', 'NTRK1', 'IRS1', 'PIK3R2', 'PIK3R3', 'GNGT1', 'MTOR', 'GRB10', 'APPL1', 'IRS2', 'GAB2', 'TICAM1', 'GNA11', 'TNF', 'AKT2', 'PIK3AP1', 'GNB1', 'GNG3', 'GNG2', 'GNG12', 'GNB3', 'SNTB2', 'NRG1', 'PIK3CD', 'MDM2', 'PIK3CG', 'NRG2', 'NRG4', 'BAK1', 'PIK3CB', 'CBFA2T3', 'ZNF652', 'NRG3', 'DLG4', 'PICK1', 'ERBB2IP', 'DLG2', 'DLG3', 'SNTA1', 'DOCK7', 'PAK1', 'PRKACA', 'PTGS2', 'ELAVL1', 'GDF15', 'RIPK1', 'FPR2', 'FPR3', 'PRKCG', 'IKBKG', 'PRKCB', 'RELA', 'TRPM7', 'PRKCH', 'SOCS1', 'APP', 'TSC1', 'SOCS3', 'PDGFRB', 'EPHB2', 'ESR2', 'NCOA2', 'MAPK9', 'MAPK8', 'MAPK10', 'NR0B2', 'EP300', 'CTNNB1', 'THRA', 'NR4A1', 'RXRB', 'RXRA', 'CDK7', 'SUMO2', 'RIF1', 'RXRG', 'MAP3K1', 'IRAK1', 'WNT5A', 'CCR2', 'IL9R', 'ECH1', 'IL20RA', 'SH2B1', 'MRPS31', 'APEX1', 'RPS9', 'DAPK3', 'PTMA', 'PKM', 'PRKCD', 'MORC4', 'CSF3R', 'SMAD3', 'IL20RB', 'CEBPB', 'IL7R', 'IL22RA1', 'PRKCE', 'CORO1A', 'MAP3K14', 'OGDHL', 'PIAS3', 'RET', 'CDKN1A', 'HDAC1', 'BCL2', 'BMX', 'IL21R', 'HDAC2', 'DNMT1', 'NFKBIZ', 'KDR', 'ALK', 'INSR', 'PIN1', 'BTK', 'NLK', 'TYK2', 'GNB2L1', 'IFNAR1', 'SULT2A1', 'TIRAP', 'BCL2L1', 'RPS6KA5', 'JAK3', 'NFKB2', 'IL15RA', 'TRIM28', 'GNL3', 'STAT4', 'BCKDK', 'BICD1', 'IL6ST', 'SRI', 'SPI1', 'FLT1', 'PIM1', 'IL11RA', 'CAPN1', 'IL10RA', 'HIF1A', 'CDK5', 'PTPRD', 'NMI', 'KLF4', 'NOS2', 'HSP90AB1', 'HSP90AA1', 'PRDM1', 'GMCL1', 'EPHB1', 'WAS', 'PAK2', 'DOK1', 'WASL', 'NCKIPSD', 'ARRB1', 'AP2S1', 'AP1B1', 'MYD88', 'RIPK2', 'TRIP6', 'TOLLIP', 'SFTPD', 'NEU1', 'CIRBP', 'TLR10', 'PSMD2', 'LY96', 'CLEC7A', 'HSP90B1', 'PRKCZ', 'CD44', 'TLR6', 'DCN', 'CD14', 'HLA-DRA', 'CYBB', 'TICAM2', 'SFTPA1', 'SNAPIN', 'TLR1', 'GJA1', 'STAT6', 'TRAF2', 'FYN', 'MET', 'CDK2', 'FKBP4', 'KIT', 'TCEB1', 'TCEB2', 'CDC42', 'CTNND1', 'SH2B2', 'ZAP70', 'ARHGAP1', 'SIAH2', 'PIDD1', 'IFI16', 'TNFRSF10A', 'NLRC4', 'FAS', 'APAF1', 'PYCARD', 'TNFRSF10B', 'DAPK1', 'GLS2', 'TYRP1', 'CX3CL1', 'BDKRB2', 'EDN2', 'ULK1', 'DDX5', 'DKK1', 'CYCS', 'CSNK2B', 'RAD51', 'NOXA1', 'PRKAA1', 'IRF9', 'CHEK1', 'CEBPZ', 'LGALS3', 'EEF1A1', 'ACTA2', 'STK11', 'IKBKB', 'BNIP3L', 'EIF2AK2', 'ETS1', 'KAT5', 'FBXW7', 'TP73', 'HNRNPK', 'IER3', 'YBX1', 'HSPA8', 'IRF5', 'PPM1D', 'CDKN2AIP', 'MAPKAPK5', 'CTSD', 'DUSP26', 'ATF3', 'PRKAB1', 'ATM', 'TOP2A', 'KRT8', 'TRAF4', 'ULK2', 'VCAN', 'DUSP5', 'USP7', 'DUSP1', 'TP53RK', 'BIRC5', 'MCL1', 'MSX1', 'BAD', 'PTEN', 'BBC3', 'FASLG', 'CSNK1D', 'TSC2', 'FANCC', 'PML', 'CASP10', 'TOP3A', 'ATR', 'CSNK1A1', 'APC', 'DYRK1A', 'CASP6', 'HGF', 'DDB2', 'BARD1', 'GADD45A', 'RB1', 'CDC25C', 'BAX', 'GRK5', 'PLK3', 'HTT', 'KDM1A', 'SIRT1', 'HIPK2', 'DHFR', 'LATS2', 'VDR', 'SERPINB5', 'BID', 'DDR1', 'SIAH1', 'NUMB', 'RPS6KA1', 'CDK9', 'SMARCB1', 'RB1CC1', 'MAPK13', 'NUAK1', 'BIRC3', 'TNFRSF10C', 'TAF1', 'TP53BP1', 'VRK1', 'SESN1', 'TP63', 'PMS2', 'HIC1', 'PPP1R13B', 'ABCB1', 'MAML1', 'CCNG1', 'CHMP4C', 'SCD', 'MDM4', 'POLK', 'IGFBP3', 'LIF', 'WRN', 'DYRK2', 'TIGAR', 'BBC3', 'BAI1', 'SETD7', 'ANLN', 'SLC38A2', 'BCL2L14', 'RRM2', 'MSL2', 'UBD', 'MSH2', 'CD82', 'NFYB', 'COL18A1', 'AIFM2', 'RRM2B', 'CDC20', 'SSBP1', 'TP53I3', 'BCL6', 'GPX1', 'PADI4', 'RPS27L', 'NOS3', 'WRAP53', 'RECQL4', 'PPP1R13L', 'ID2', 'TP53INP1', 'BLM', 'MAD1L1', 'ARID3A', 'RGCC', 'SIRT7', 'SCARA3', 'MLH1', 'TP53AIP1', 'TRIM22', 'ODC1', 'SMYD2', 'TRIAP1', 'PMAIP1', 'ASCC3', 'SCN3B', 'TAP1', 'FDXR', 'GTSE1', 'TRPM2', 'DDIT4', 'REV3L', 'KAT6A', 'NFYA', 'CHEK2', 'STEAP3', 'TNFRSF10D', 'TOP2B', 'PRC1', 'MIR17HG', 'SERPINE1', 'ERCC6', 'NDRG1', 'BTG2', 'ING2', 'RNF144B', 'RFWD2', 'GML', 'EPHA2', 'PLAGL1', 'PLK2', 'SH2D1A', 'SMG1', 'AURKB', 'XPC', 'AURKA', 'S100A2', 'TP53BP2', 'PCBP4', 'MYCN', 'HTATIP2', 'PERP', 'P2RX6', 'PTTG1', 'P4HA2', 'TTK', 'CCNK', 'PPM1J', 'ZNF420', 'ING1', 'CRYZ', 'RABGGTA', 'GMPS', 'TRIM24', 'STK17A', 'CDKN2A', 'FBXO11', 'TOPORS', 'AR', 'FOXO1', 'PDPK1', 'MAPT', 'PGM1', 'ARHGEF2', 'RAF1', 'PPP1R14A', 'ZAK', 'SNAI1', 'PGAM1', 'YWHAZ', 'MAP3K6', 'EPOR', 'AXL', 'FRS2', 'TEK', 'FGFR2', 'VAV1', 'IRS4', 'MST1R', 'CSF2RB', 'CD33', 'SIGLEC7', 'MAP3K5', 'IRF8', 'SIGLEC5', 'SIRPA', 'CTNNA1', 'SELE', 'BTLA', 'SIGLEC10', 'PXN', 'HOXA10', 'TERT', 'MPZL1', 'UBC', 'CARD16', 'CARD17', 'NOD1', 'NLRP1', 'CARD18', 'MAVS', 'CARD8', 'NLRP2', 'NLRP10', 'NLRP3', 'NLRP7', 'NOD2', 'IL1A', 'CASP5', 'FGF2', 'SREBF2', 'IL1B', 'IL33', 'IL37', 'ARHGDIA', 'GZMB', 'MEFV', 'PLA2G4A', 'TRIM16L', 'CASP4', 'ALDOA', 'PYDC1', 'ENO1', 'DDX58', 'IL18', 'TPI1', 'SERPINB9', 'CASP12', 'TRPC1', 'GSK3B', 'PEA15', 'ADAM17', 'AGTR1', 'MAP4K1', 'MAP3K2', 'FHL3', 'FHL1', 'PPARG', 'NUP153', 'IL16', 'STAB2', 'RPS6KA2', 'RORA', 'SP1', 'MYC', 'CSNK2A1', 'KHDRBS1', 'WWC1', 'KLC1', 'DUSP4', 'CTTN', 'CASP8', 'NFATC4', 'DUSP3', 'KCND2', 'SNCA', 'DUSP9', 'KLF11', 'HSF4', 'NFE2L2', 'SNCG', 'CAPN2', 'TNIP1', 'CREBBP', 'CDKN1B', 'MAP3K10', 'SMAD2', 'DYRK1B', 'RPS6KA3', 'ATF2', 'JUND', 'MAP2K3', 'JUN', 'RUNX1', 'ARAF', 'ELK1', 'PARP1', 'MAP2K2', 'BRAF', 'NEK2', 'PRDX6', 'FHL2', 'RPTOR', 'IQGAP1', 'FGFR1', 'SMAD1', 'EIF4EBP1', 'HSF1', 'PPP1CA', 'ITGB6', 'SLC9A1', 'RPS6KA4', 'SLC2A4', 'RPS6KB1', 'PTPRB', 'HDAC4', 'CASP9', 'C1QBP', 'MKNK2', 'PTPN7', 'PPP2CA', 'BCL2L11', 'FOXO3', 'ADAM15', 'SQSTM1', 'GORASP2', 'MKNK1', 'LRP6', 'THRB', 'NCF1', 'PGR', 'SORBS3', 'STMN1', 'CAD', 'MAPKAPK2', 'LAMTOR3', 'DUSP6', 'SREBF1', 'DUSP16', 'GABPA', 'RPS3', 'DUSP2', 'BMF', 'SPHK1', 'H3F3B', 'CALD1', 'SMAD4', 'ARRB2', 'NEFH', 'PPP2R5C', 'PLAA', 'MARCKS', 'RGS19', 'MITF', 'MBP', 'PTPN5', 'MEF2B', 'SYN1', 'CNKSR1', 'NEFM', 'PDE4D', 'KHDRBS2', 'CARD14', 'AMPH', 'SP3', 'POLR2A', 'GTF2I', 'MTNR1A', 'SPHK2', 'TUB', 'ABI1', 'ESPL1', 'NCOA1', 'CEBPA', 'LIFR', 'TWIST1', 'APBB1', 'STIM1', 'EWSR1', 'CIC', 'PITPNM1', 'PDE4C', 'TFCP2', 'ERF', 'MAFA', 'DUSP7', 'MED1', 'CIITA', 'NR4A2', 'PCYT1A', 'PTPRJ', 'NUP50', 'POU5F1', 'UBTF', 'MKL1', 'CEP55', 'TH', 'TPR', 'TOB1', 'EXOC7', 'NOX5', 'TCL1A', 'ELF1', 'CGA', 'NFAT5', 'CXCL12', 'IGF1', 'TXN', 'GATA3', 'TRIM25', 'DDX17', 'NFKB1', 'HNF1A', 'CHUK', 'IKBKE', 'HSPD1', 'WIPI1', 'XBP1', 'SLC2A1', 'TDG', 'FAM102A', 'MTA1', 'MPG', 'MAT1A', 'TSKU', 'ATAD2', 'TFF1', 'NME1', 'EBAG9', 'INA', 'IGFBP4', 'B4GALT1', 'POU4F2', 'POU4F1', 'KMT2D', 'YAP1', 'YTHDC1', 'BRCA1', 'MYLK', 'CAT', 'CD19', 'RYBP', 'PSTPIP1', 'SPAG9', 'PSMA7', 'ABL2', 'NEDD9', 'LASP1', 'STK3', 'SORBS2', 'WASF3', 'PRKD1', 'NFKBIA', 'STK4', 'NCOA3', 'HCLS1', 'BCAR1', 'CLK1', 'CRKL', 'BCR', 'HCK', 'RAPGEF1', 'MSH5', 'DNM2', 'WASF2', 'CHRNB1', 'PARK2', 'PLSCR1', 'RAD9A', 'RAPH1', 'TRIP10', 'ZDHHC16', 'TOP1', 'ROBO1', 'SYNJ2', 'POLR2B', 'CDV3', 'ARHGAP35', 'SRCIN1', 'CLK4', 'RFX1', 'SPTLC1', 'CDON', 'PROKR1', 'EIF4G2', 'PTGES3', 'HNRNPD', 'DFFA', 'BTRC', 'EIF4G3', 'AKT3', 'CD247', 'EIF4B', 'VIM', 'RBX1', 'PTCH1', 'TCP10L', 'COPS6', 'XIAP', 'HDAC7', 'FBXW11', 'GZMM', 'RNF7', 'ATG4D', 'ROCK1', 'GSN', 'EIF4G1', 'BIRC2', 'AFP', 'NAIP', 'PIP4K2A', 'EIF3J', 'BIRC6', 'DFFB', 'ACIN1', 'EIF2S2', 'GORASP1', 'NUMA1', 'SPTAN1', 'HSPB2', 'EIF2S3', 'EIF2A', 'PSIP1', 'CASP2', 'PPP2R5B', 'GAS2', 'NTRK2', 'ACTN1', 'CD36', 'PKD1', 'ITGB1', 'ACTN4', 'CAMK2A', 'FGR', 'CSK', 'ACTN3', 'PTPN12', 'SH3GL1', 'TAB1', 'DUSP10', 'MAP2K6', 'MAP2K4', 'TCF3', 'HBP1', 'IRAK4', 'AHSG', 'SIGIRR', 'NOX4', 'TLR5', 'STK11IP', 'MBL2', 'TRAF3', 'MAL', 'UBQLN1', 'TMED7', 'LY86', 'MAP3K8', 'TREM1', 'HSPA14', 'CNPY3', 'SYK', 'SFTPA2', 'F2RL1', 'RNF216', 'GRIN2A', 'GPHN', 'MAP1B', 'MAP2', 'CRIPT', 'DNM1', 'GABARAPL3', 'DPYSL2', 'MAP1A', 'TTL', 'RNF111', 'AAK1', 'TRAF6', 'PDGFRA', 'CD40', 'STX3', 'TRPC4', 'ITGAX', 'PLCG2', 'PNRC1', 'SOS2', 'DAB2', 'LY9', 'MERTK', 'CD300LB', 'CD28', 'TGFBR2', 'CD22', 'LAT2', 'SELL', 'PSEN1', 'PTPRA', 'SH3KBP1', 'REPS1', 'DRD3', 'RBP1', 'A9UF07', 'TGFB1', 'PDGFB', 'PDGFA', 'IGF2', 'ID3', 'NFATC1', 'MAP1LC3B', 'NAB2', 'NAB1', 'TOPBP1', 'SFPQ', 'RHEB', 'POU2F1', 'GLRX', 'EDN1', 'NONO', 'TRPC3', 'TRPC6', 'TRPC5', 'ISG15', 'CRLF2', 'GHR', 'CSF2RA', 'PRLR', 'NR3C1', 'MPL', 'CISH', 'IL2RG', 'IL3RA', 'CTLA4', 'IL2RB', 'IL5RA', 'CSN2', 'CNOT8', 'IRF1', 'IFNAR2', 'NUP214', 'MBD1', 'IFNGR1', 'HDAC3', 'KPNA6', 'STAT2', 'ARNT', 'IFNGR2', 'SRF', 'PIAS4', 'KPNA1', 'PIAS1', 'DDB1', 'ANO9', 'MDC1', 'IRGC', 'CAMK2B', 'INPP5D', 'CD72', 'MS4A2', 'PPP1R8', 'PLAUR', 'RPL10', 'PPP1R15A', 'FCGR2A', 'CDK4', 'NMT1', 'LIME1', 'TRPV4', 'SLAMF1', 'PBK', 'DLG1', 'PTHLH', 'WEE1', 'LMNA', 'RANGAP1', 'HMGA2', 'NSFL1C', 'CDC25B', 'MAP4', 'KRT18', 'RUNX2', 'EZH2', 'NUP98', 'DDX3X', 'FOXM1', 'LATS1', 'RAP1GAP', 'CDC27', 'NPM1', 'SAMHD1', 'PRDX1', 'PLEC', 'ANAPC1', 'EEF2K', 'PIK3C3', 'KAT7', 'INCENP', 'FANCG', 'UBE2A', 'LIG1', 'SIRT2', 'ECT2', 'FEN1', 'MCM3', 'SETD8', 'USP16', 'HMGA1', 'KIF11', 'BORA', 'ESCO1', 'BUB1', 'CDC7', 'MCM4', 'KIF2C', 'RPA2', 'CDK5RAP3', 'PKMYT1', 'NDEL1', 'BUB1B', 'MYBL2', 'E2F4', 'FBXO5', 'MAPK6', 'CDC25A', 'MYOD1', 'CKS1B', 'NDE1', 'IREB2', 'GOLGA2', 'KIF22', 'ZC3HC1', 'ERCC6L', 'LBR', 'PIK3C2A', 'TK1', 'UBA1', 'CKAP2', 'CDC16', 'ORC1', 'EEF1D', 'MPLKIP', 'APLP2', 'NUSAP1', 'CUX1', 'RAB5B', 'SYN3', 'FOXK2', 'CDC23', 'PLCB3', 'F11R', 'PHLPP2', 'TIAM1', 'PLD2', 'IL2RA', 'PFKFB3', 'PRKG1', 'GSK3A', 'ADAP1', 'CFL1', 'HNRNPA1', 'RPS6KB2', 'AQP1', 'EGLN2', 'PARD6A', 'PHLPP1', 'ADRBK1', 'PLEK', 'RASGRP3', 'EIF4E', 'NR1H4', 'CLIP1', 'ATP2B1', 'PLD1', 'PLCB1', 'ADD1', 'GLRA1', 'CACNA1B', 'CACNA1C', 'ADCY5', 'AKAP5', 'GNAZ', 'GRIK1', 'GABRA1', 'GRM7', 'NOS1', 'NFASC', 'GRM1', 'ADCY2', 'PDE3A', 'DGUOK', 'GAP43', 'GRIA1', 'SNAP25', 'CDKN2D', 'RALB', 'HMGN1', 'HMGN2', 'NKX3-1', 'MYL9', 'TNNI3', 'TRPV5', 'CASR', 'KCNMA1', 'TRPM4', 'NPHS1', 'HRH1', 'PIP5K1B', 'CORO1B', 'LRP1', 'DVL1P1', 'ACO1', 'ARHGDIB', 'KCNJ13', 'THOC5', 'CHAT', 'CD5', 'ADD2', 'CTPS1', 'NOXO1', 'HSPB8', 'F3', 'GRIA4', 'EIF6', 'CFLAR', 'LTK', 'SH3GLB1', 'SORBS1', 'PTPN22', 'UBASH3B', 'RAC2', 'RND1', 'ARPC1B', 'ANAPC11', 'ITGAE', 'ITGB7', 'ZFYVE9', 'MAP3K7', 'TYRO3', 'WBP11', 'TSHR', 'TGFBR1', 'FLT3', 'LCP2', 'RHOG', 'GNAS', 'TLR3', 'IL1R1', 'FLNB', 'FLNA', 'PTPRF', 'FLNC', 'ITK', 'RHOA', 'NTRK3', 'RRAS', 'GIT1', 'TRPM6', 'TNFRSF1A', 'IL4R', 'PTPRC', 'IFNB1', 'LEPR', 'IFNLR1', 'IL31RA', 'GLI1', 'KSR1', 'BRAP', 'KSR2', 'PEBP1', 'WDR83', 'TAL1', 'ETV6', 'ZFP36L1', 'ELK4', 'MAGEA11', 'MYL1', 'LAT', 'MYB', 'BAZ1B', 'MAZ', 'KARS', 'SPIB', 'SULT4A1', 'RRN3', 'CXCR4', 'IL13RA1', 'DNAJA3', 'STAM', 'IL23R', 'IL12RB1', 'ARHGEF1', 'HIST1H3B', 'PRMT5', 'NIN', 'ADRB2', 'ROR1', 'EMD', 'CDH5', 'INPPL1', 'SMO', 'RUNX3', 'CLTC', 'ARHGAP32', 'VIL1', 'PDK1', 'BMPR2', 'ANXA2', 'WWOX', 'PRKCI', 'FLT4', 'TRAF1', 'HNF4A', 'CDH2', 'MUSK', 'SPTBN2', 'MMP14', 'TNS3', 'NOX1', 'UGT2B7', 'TRPV6', 'CHN2', 'CHRNA7', 'PROM1', 'DGKA', 'CYP19A1', 'KRT19', 'HLA-A', 'PTPN21', 'KCNA3', 'KCNJ1', 'DOK4', 'DDR2', 'GLRB', 'ARHGEF4', 'AP2B1', 'PIP5K1C', 'VAV3', 'HCN4', 'DAG1', 'KCNB1', 'EPHA3', 'MMP3', 'CDK8', 'CCNB1', 'CCNA2', 'YWHAQ', 'HSPA5', 'EED', 'MAP1LC3A', 'XRCC1', 'MCPH1', 'CDT1', 'CCNA1', 'E2F6', 'POLA1', 'CDKN2A', 'DTL', 'DBF4', 'DAPK2', 'CDCA4', 'TNK2', 'FADD', 'L1CAM', 'FES', 'STK26', 'CCR5', 'PTK6', 'PTPRE', 'ARHGEF7', 'HBA1', 'KCNH2', 'CD46', 'PILRA', 'LILRB1', 'ROS1', 'LAIR1', 'KIR2DL1', 'ACTG1', 'SIGLEC9', 'LILRB4', 'LILRB2', 'CEACAM1', 'SH3BP2', 'MAPK15', 'CLK2', 'CUL1', 'NOTCH1', 'EHMT1', 'FBXO31', 'CDK6', 'FBXW8', 'MLLT4', 'RLF', 'RALGDS', 'YWHAH', 'SEC31A', 'MCOLN1', 'CD74', 'HLA-DMB', 'SAR1A', 'HLA-DMA', 'B2M', 'SEC24A', 'SEC23A', 'HLA-DRB1', 'PTPN4', 'DOCK1', 'KCNA2', 'GNA13', 'CARD9', 'MAP3K4', 'PPM1A', 'MAPKAPK3', 'GATA2', 'USF1', 'DDIT3', 'MAPKAP1', 'MEF2D', 'PLCB2', 'STK39', 'MAP3K11', 'TIAL1', 'MAX', 'SMAD7', 'MAPK8IP1', 'CDKN1C', 'PPARGC1A', 'MAPK8IP2', 'MEF2A', 'MAP4K3', 'MINK1', 'ELK3', 'ZFP36', 'CCND2', 'DUSP8', 'PIP4K2B', 'EEA1', 'RBSN', 'ZNHIT1', 'PTPRR', 'SMARCD3', 'CSNK2A2', 'MEF2C', 'PAK6', 'PPP3CA', 'PPP3CB', 'ADCY1', 'CAMKK2', 'CAMK4', 'RYR1', 'VAPA', 'PDE1B', 'RIT2', 'RAB3A', 'DRD2', 'RASGRF1', 'UNC13B', 'PDE1A', 'MYRIP', 'ITPR1', 'PDE1C', 'MYO6', 'PPEF2', 'MYO1C', 'CAMKK1', 'TRPM3', 'TRPV2', 'PPP3CC', 'BAIAP2', 'SRGAP3', 'XRCC5', 'IRF3', 'HNRNPU', 'UPF1', 'XRCC6', 'VCP', 'TELO2', 'PNKP', 'TDP1', 'HERC2', 'HIST1H1A', 'RPA1', 'DCLRE1C', 'TTI1', 'CCNT2', 'SMC1A', 'H2AFX', 'HINFP', 'EIF2AK4', 'NHEJ1', 'LIG4', 'HOXB7', 'GNAI1', 'NRF1', 'TUBA4B', 'SRSF2', 'UBE2N', 'ERCC5', 'CHAF1B', 'CHAF1A', 'POLD2', 'FANCD2', 'E2F2', 'HUS1', 'SHPRH', 'USP1', 'RFC1', 'POLD1', 'RAD18', 'CLSPN', 'MSH6', 'POLD4', 'POLI', 'TIMELESS', 'MUTYH', 'EXO1', 'POLH', 'TRPA1', 'PPARA', 'SYT1', 'PRKAA2', 'FAF1', 'PRKCSH', 'CNR1', 'GABARAP', 'SCNN1A', 'KCNQ3', 'KCNQ2', 'KIF13B', 'SYT4', 'PACS1', 'PIRT', 'KCNAB2', 'GRIN1', 'PRKAR2A', 'GRIN2B', 'IFT57', 'ACTN2', 'CBY1', 'WWTR1', 'HAX1', 'PSMD7', 'EIF2AK3', 'EIF2S1', 'DIAPH1', 'TPM1', 'HAVCR1', 'CD2AP', 'STX5', 'TNNI1', 'TRPC7', 'KIF3B', 'PKHD1', 'AP1G1', 'PCNT', 'RP2', 'RYR2', 'PACS2', 'NEK8', 'TNNI2', 'KIF3A', 'GNAQ', 'TRIM27']

7: Accessing the literature references

References are listed in the references edge attribute:

In [49]:
[<pypath.input_formats.Reference object at 0x7f1a19b52350>, <pypath.input_formats.Reference object at 0x7f1a143d6410>, <pypath.input_formats.Reference object at 0x7f1a1436a350>, <pypath.input_formats.Reference object at 0x7f1a177972d0>]

Each reference has its PubMed ID:

In [45]:
Out[45]:
'2186024'

To open in a browser just call open():

In [ ]:

It's possible to know which resources cite which papers:

In [50]:
Out[50]:
{'SPIKE': [<pypath.input_formats.Reference at 0x7f1a177972d0>],
 'SignaLink3': [<pypath.input_formats.Reference at 0x7f1a19b52350>],
 'Signor': [<pypath.input_formats.Reference at 0x7f1a143d6410>,
  <pypath.input_formats.Reference at 0x7f1a1436a350>],
 'egf1': [],
 'egf2': []}

8: Direction objects

Each edge stores its direction and effect sign data in one Direction object:

In [62]:
Out[62]:
<pypath.main.Direction at 0x7f1a24344650>

Also there are ways to query the direction and effect information by resources:

In [53]:
Out[53]:
{'SPIKE', 'SignaLink3', 'Signor', 'egf1', 'egf2'}

reverse means an arbitrary direction, noted as a tuple of UniProt IDs, where UniProt ID #1 affects UniProt ID #2; straight is its opposite, and undirected means unknown direction:

In [57]:
('P01133', 'P00533')
('P00533', 'P01133')

By default, get_dirs() returns boolean values:

In [60]:
Out[60]:
True

The same way effect signs can be queried. A pair of boolean values means if the interaction is stimulation and if it is inhibition, respectively.

In [61]:
Out[61]:
[True, True]
In [ ]: