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Updated sections file to version used for paper.
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dvklopfenstein committed Jun 27, 2018
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164 changes: 164 additions & 0 deletions goatools/test_data/sections/gjoneska_pfenning.py
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"""Sections variable used for grouping Gjoneska 2015 GO IDs."""

__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved."
__author__ = "DV Klopfenstein"


SECTIONS = [ # 18 sections
("immune", [ # 15 GO-headers
"GO:0002376", # BP 564 L01 D01 M immune system process
"GO:0002682", # BP 1,183 L02 D02 AB regulation of immune system process
"GO:0030155", # BP 246 L02 D02 AB regulation of cell adhesion
"GO:0006955", # BP 100 L02 D02 GM immune response
"GO:0001817", # BP 476 L03 D03 AB regulation of cytokine production
"GO:0001775", # BP 162 L03 D03 CD cell activation
"GO:0001816", # BP 110 L03 D03 DK cytokine production
"GO:1903037", # BP 155 L04 D04 AB regulation of leukocyte cell-cell adhesion
"GO:0034097", # BP 59 L04 D04 G response to cytokine
"GO:0006954", # BP 25 L04 D04 G inflammatory response
"GO:0045087", # BP 25 L03 D04 GM innate immune response
"GO:0002521", # BP 72 L05 D05 CDF leukocyte differentiation
"GO:0007229", # BP 0 L05 D05 AB integrin-mediated signaling pathway
"GO:0050900", # BP 57 L02 D06 CDMN leukocyte migration
"GO:0042130", # BP 9 L07 D08 AB negative regulation of T cell proliferation
#"GO:0002252", # BP 138 L02 D02 L immune effector process
]),
("viral/bacteria", [ # 4 GO-headers
"GO:0016032", # BP 301 L03 D04 CJ viral process
"GO:0050792", # BP 119 L03 D04 AB regulation of viral process
"GO:0098542", # BP 37 L03 D05 GJ defense response to other organism
"GO:0009617", # BP 12 L03 D05 GJ response to bacterium
]),
("neuro", [ # 25 GO-headers
"GO:0099531", # BP 32 L01 D01 U presynaptic process in chemical synaptic Xmission
"GO:0042391", # BP 117 L03 D03 A regulation of membrane potential
"GO:0050877", # BP 96 L03 D03 K neurological system process
"GO:0050808", # BP 20 L03 D03 CDI synapse organization
"GO:0007272", # BP 13 L03 D03 CD ensheathment of neurons
"GO:0051960", # BP 236 L04 D04 AB regulation of nervous system development
"GO:0050804", # BP 120 L03 D04 AB modulation of synaptic transmission
"GO:0097485", # BP 34 L04 D04 CD neuron projection guidance
"GO:0031644", # BP 30 L04 D04 AB regulation of neurological system process
"GO:0031175", # BP 14 L04 D04 CDI neuron projection development
"GO:0035418", # BP 14 L04 D04 H protein localization to synapse
"GO:0007399", # BP 0 L04 D04 F nervous system development
"GO:0050767", # BP 192 L05 D05 AB regulation of neurogenesis
"GO:0030182", # BP 71 L05 D05 CDF neuron differentiation
"GO:0099536", # BP 40 L04 D05 CDR synaptic signaling
"GO:0048666", # BP 29 L04 D05 CDF neuron development
"GO:0010001", # BP 17 L05 D05 CDF glial cell differentiation
"GO:0051969", # BP 5 L03 D05 AB regulation of transmission of nerve impulse
"GO:0022008", # BP 3 L05 D05 CDF neurogenesis
"GO:0007158", # BP 0 L04 D05 DP neuron cell-cell adhesion
"GO:0014002", # BP 1 L05 D06 CDF astrocyte development
"GO:0048812", # BP 27 L05 D07 CDFI neuron projection morphogenesis
"GO:0048667", # BP 6 L06 D07 CDFI cell morphogenesis involved in neuron differen.
"GO:0072578", # BP 5 L05 D07 CDHI neurotransmitter-gated ion channel clustering
"GO:0007409", # BP 23 L06 D08 CDFI axonogenesis
]),
("cell death", [ # 6 GO-headers
"GO:0010941", # BP 316 L03 D03 AB regulation of cell death
"GO:0008219", # BP 104 L03 D03 CD cell death
"GO:0060548", # BP 103 L04 D04 AB negative regulation of cell death
"GO:0097190", # BP 22 L04 D04 AB apoptotic signaling pathway
"GO:0097527", # BP 0 L04 D04 AB necroptotic signaling pathway
"GO:0008637", # BP 7 L05 D05 CI apoptotic mitochondrial changes
]),
("lipid", [ # 7 GO-headers
"GO:0006629", # BP 623 L03 D03 DE lipid metabolic process
"GO:0019216", # BP 243 L04 D04 AB regulation of lipid metabolic process
"GO:0032368", # BP 130 L04 D04 AB regulation of lipid transport
"GO:0033993", # BP 112 L04 D04 G response to lipid
"GO:0006869", # BP 93 L04 D05 DH lipid transport
"GO:0055088", # BP 10 L05 D05 A lipid homeostasis
"GO:0042158", # BP 3 L05 D06 CE lipoprotein biosynthetic process
]),
("adhesion", [ # 3 GO-headers
"GO:0022610", # BP 194 L01 D01 P biological adhesion
"GO:0030155", # BP 246 L02 D02 AB regulation of cell adhesion
"GO:0007155", # BP 165 L02 D02 P cell adhesion
]),
("cell cycle", [ # 9 GO-headers
"GO:0022402", # BP 463 L02 D02 C cell cycle process
"GO:0022403", # BP 46 L02 D02 S cell cycle phase
"GO:0051726", # BP 411 L03 D03 AB regulation of cell cycle
"GO:0051301", # BP 54 L03 D03 CD cell division
"GO:0007049", # BP 12 L03 D03 CD cell cycle
"GO:0070192", # BP 17 L03 D05 CIL chromosome organization in meiotic cell cycle
"GO:0007051", # BP 19 L03 D06 CDI spindle organization
"GO:0007067", # BP 1 L04 D06 CI mitotic nuclear division
"GO:0030071", # BP 11 L06 D09 AB regulation of mitotic metaphase/anaphase transition
]),
("chromosome", [ # 9 GO-headers
"GO:0032259", # BP 119 L02 D02 E methylation
"GO:0051983", # BP 108 L03 D03 AB regulation of chromosome segregation
"GO:0007059", # BP 11 L03 D03 CD chromosome segregation
"GO:0006325", # BP 184 L04 D04 CI chromatin organization
"GO:0051276", # BP 107 L04 D04 CI chromosome organization
"GO:0032204", # BP 29 L03 D06 AB regulation of telomere maintenance
"GO:0034502", # BP 21 L06 D06 H protein localization to chromosome
"GO:0031497", # BP 11 L05 D06 CI chromatin assembly
"GO:0006334", # BP 3 L06 D07 CI nucleosome assembly
]),
("development", [ # 10 GO-headers
"GO:0032502", # BP 3,173 L01 D01 F developmental process
"GO:0022414", # BP 847 L01 D01 L reproductive process
"GO:0050793", # BP 1,881 L02 D02 AB regulation of developmental process
"GO:0048856", # BP 1,016 L02 D02 F anatomical structure development
"GO:0048646", # BP 331 L02 D02 F anatomical structure formation in morphogenesis
"GO:0007568", # BP 18 L03 D03 DF aging
"GO:0022604", # BP 129 L04 D04 AB regulation of cell morphogenesis
"GO:0000902", # BP 65 L04 D05 CDFI cell morphogenesis
"GO:0045765", # BP 14 L04 D05 AB regulation of angiogenesis
]),
("extracellular matrix", [ # 1 GO-headers
"GO:0030198", # BP 27 L04 D04 CDI extracellular matrix organization
]),
("ion", [ # 3 GO-headers
"GO:0006811", # BP 422 L04 D04 H ion transport
"GO:0055085", # BP 330 L04 D04 H transmembrane transport
"GO:0006874", # BP 33 L08 D09 ACD cellular calcium ion homeostasis
]),
("localization", [ # 3 GO-headers
"GO:0051179", # BP 2,142 L01 D01 H localization
"GO:0040011", # BP 394 L01 D01 N locomotion
"GO:0032879", # BP 1,682 L02 D02 AB regulation of localization
]),
("membrane", [ # 1 GO-headers
"GO:0061024", # BP 273 L03 D03 CI membrane organization
]),
("metabolic", [ # 7 GO-headers
"GO:0008152", # BP 6,418 L01 D01 E metabolic process
"GO:0019222", # BP 3,243 L02 D02 AB regulation of metabolic process
"GO:0009056", # BP 1,369 L02 D02 E catabolic process
"GO:0044281", # BP 2,139 L03 D03 DE small molecule metabolic process
"GO:0050790", # BP 620 L03 D03 A regulation of catalytic activity
"GO:0051186", # BP 373 L03 D03 CE cofactor metabolic process
"GO:0006259", # BP 300 L04 D06 CE DNA metabolic process
]),
("phosphorylation", [ # 3 GO-headers
"GO:0006793", # BP 798 L03 D03 CE phosphorus metabolic process
"GO:0016310", # BP 138 L05 D05 CE phosphorylation
"GO:0006468", # BP 97 L06 D07 CE protein phosphorylation
]),
("signaling", [ # 4 GO-headers
"GO:0023052", # BP 116 L01 D01 R signaling
"GO:0023051", # BP 1,364 L02 D02 AB regulation of signaling
"GO:0007165", # BP 717 L03 D03 AB signal transduction
"GO:0007267", # BP 99 L03 D04 CDR cell-cell signaling
]),
("stimulus", [ # 4 GO-headers
"GO:0050896", # BP 2,218 L01 D01 G response to stimulus
"GO:0048583", # BP 2,377 L02 D02 AB regulation of response to stimulus
"GO:0006950", # BP 492 L02 D02 G response to stress
"GO:0080134", # BP 940 L03 D03 AB regulation of response to stress
]),
("prolif_differ", [ # 3 GO-headers
"GO:0008283", # BP 158 L02 D02 D cell proliferation
"GO:0030154", # BP 494 L04 D04 CDF cell differentiation
"GO:0045595", # BP 828 L03 D03 AB regulation of cell differentiation
"GO:0042127", # BP 268 L03 D03 AB regulation of cell proliferation
]),
]

# Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved.

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