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Module #727, TG: 2.6, TC: 2, 123 probes, 123 Entrez genes, 5 conditions
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The image plot shows the color-coded level of gene expression, for the
genes and conditions in a given transcription module. The genes are on
the horizontal, the conditions on the vertical axis.
The genes are ordered according to their ISA gene scores, similarly
the conditions are ordered according to their condition scores. The
score of a gene means the «degree of inclusion» in
the module: a high score gene is essential in the module.
Condition scores can also be negative, that means that the genes of
the module are all down-regulated in the condition. Here the absolute
value of the score gives the «degree of inclusion».
The plots above and beside the expression matrix show the gene scores
and condition scores, respectively.
Note that the plot is interactive, you can see the name of the gene
and condition under the mouse cursor.
The expression matrix was normalized to have mean zero and standard
deviation one for every gene separately across all conditions
(i.e. not just for the conditions in the module).
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Under-expression is coded with green,
over-expression with red color.
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The GO tree — Biological processes
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This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for biological processes.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
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The GO tree — Cellular Components
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for cellular components.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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The GO tree — Molecular Function
HELP
This is one of three sections showing Gene Ontology enrichment of the
current module: in this case for molecular function.
The graph shows the hierarchy of the GO categories, their enrichment
for the current module is color coded, and the blue number beside the
category is the minus log ten p-value of the enrichment. (Calculated
using the standard hypergeometric test.) The color of the arrows code
«is a» (cyan) and «part of» relationships.
The tree was built the following way. First all GO terms with more
significant enrichment p-value than 0.05 were collected. Then all
paths from these terms to the root node of the GO tree were included
too. If a GO term is included more than once in the tree, then the
green numbers show 1) the id of the node, this makes it easier to find
other appereances of the term, and 2) the number of appearences.
Note that the same GO category might show up on the graph many
times. This is because the GO was «straightened» for this
graph, i.e. if there are more paths from a GO term to the root node of
the tree, all of them are included. The green numbers
Move the mouse cursor over the terms to get their definition. Clicking
on them takes you to the corresponding Gene Ontology web page.
If you cannot see a graph here at all, that means that there were no
significantly enriched GO categories, at the 0.05 level.
— Click on the Help button again to close this help window.
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GO BP test for over-representation
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List of all enriched GO categories (biological processes), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0008298 | 3.004e-02 | 0.03783 | 2
CASC3, STAU1 | 3 | intracellular mRNA localization |
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GO CC test for over-representation
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List of all enriched GO categories (cellular components), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
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| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0031092 | 3.627e-02 | 0.06307 | 2
GP1BA, GP1BB | 5 | platelet alpha granule membrane |
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GO MF test for over-representation
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List of all enriched GO categories (molecular function), at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given GO term, just by chance.
- Count
is the number of genes in the module annotated with the given GO
term.
- Size is the total number of genes (in our universe)
annotated with the GO term.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
GO category.
Clicking on the GO identifiers takes you to the Gene Ontology web
pages.
— Click on the Help button again to close this help window.
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KEGG Pathway test for over-representation
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List of all enriched KEGG pathways, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module annotated with the given KEGG pathway, just by chance.
- Count
is the number of genes in the module annotated with the given KEGG
pathway.
- Size is the total number of genes (in our universe)
annotated with the KEGG pathway.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
KEGG pathway.
Clicking on the KEGG identifiers takes you to the KEGG web site.
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miRNA test for over-representation
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List of all enriched miRNA families, at the 0.05
p-value level.
The columns:
- ExpCount is the expected count of genes in the
module regulated by the given miRNA family, just by chance.
- Count
is the number of genes in the module regulated by the given miRNA
family.
- Size is the total number of genes (in our universe)
regulated with the given miRNA family.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
miRNA family.
The miRNA regulation data was taken from the TargetScan database.
(Only the conserved sites were used for the current analysis.)
Clicking on the miRNA names takes you to the TargetScan web site.
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Chromosome test for over-representation
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List of all enriched Chromosomes, at the 0.05
p-value level.
The columns:
- ExpCount is the expected number of genes in the
module on the given chromosome, just by chance.
- Count
is the number of genes in the module on the given chromosome.
- Size is the total number of genes (in our universe)
on the given chromosome.
Clicking on Count shows the genes that drive the
enrichment. You can also click on the individual numbers in
the Count column, to show the driving genes for that individual
chromosome.
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HELP
A list of all genes in the current module, in alphabetical order. The
size of the text corresponds to the gene scores.
Note that some gene symbols may show up more than once, if many
probes match the same Entrez gene.
Genes with no Entrez mapping are given separately, with their
Affymetrics probe ID.
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Entrez genes
ABLIM1actin binding LIM protein 1 (200965_s_at), score: 0.64
ADCK2aarF domain containing kinase 2 (221893_s_at), score: 0.68
ADCY3adenylate cyclase 3 (209321_s_at), score: 0.98
AKAP2A kinase (PRKA) anchor protein 2 (202759_s_at), score: 0.64
ANAPC2anaphase promoting complex subunit 2 (218555_at), score: 0.66
ARHGAP22Rho GTPase activating protein 22 (206298_at), score: 0.68
ARL17P1ADP-ribosylation factor-like 17 pseudogene 1 (210718_s_at), score: 0.65
ARNTLaryl hydrocarbon receptor nuclear translocator-like (209824_s_at), score: 0.68
ATN1atrophin 1 (40489_at), score: 0.69
BIN1bridging integrator 1 (210201_x_at), score: 0.71
BRCA2breast cancer 2, early onset (208368_s_at), score: -0.78
C16orf57chromosome 16 open reading frame 57 (218060_s_at), score: 0.68
C20orf111chromosome 20 open reading frame 111 (209020_at), score: -0.69
C7orf25chromosome 7 open reading frame 25 (53202_at), score: -0.69
CASC3cancer susceptibility candidate 3 (207842_s_at), score: 0.67
CDC42BPBCDC42 binding protein kinase beta (DMPK-like) (217849_s_at), score: 0.76
CDR2Lcerebellar degeneration-related protein 2-like (213230_at), score: 0.78
CENPQcentromere protein Q (219294_at), score: -0.67
CHST2carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 (203921_at), score: 0.77
CICcapicua homolog (Drosophila) (212784_at), score: 0.66
CLCN2chloride channel 2 (213499_at), score: -0.72
COL10A1collagen, type X, alpha 1 (217428_s_at), score: 0.84
COL18A1collagen, type XVIII, alpha 1 (209081_s_at), score: 0.68
CORO2Bcoronin, actin binding protein, 2B (209789_at), score: 0.76
CRTC3CREB regulated transcription coactivator 3 (218648_at), score: 0.78
DENND4BDENN/MADD domain containing 4B (202860_at), score: 0.83
DKFZP586I1420hypothetical protein DKFZp586I1420 (213546_at), score: -0.7
DNM3dynamin 3 (209839_at), score: 0.63
DOK4docking protein 4 (209691_s_at), score: 0.62
EML2echinoderm microtubule associated protein like 2 (204398_s_at), score: -0.72
EPHA4EPH receptor A4 (206114_at), score: -0.73
F11coagulation factor XI (206610_s_at), score: -0.79
FAM168Bfamily with sequence similarity 168, member B (212017_at), score: 0.66
FAM3Afamily with sequence similarity 3, member A (38043_at), score: 0.66
FASNfatty acid synthase (212218_s_at), score: 0.69
FBXO17F-box protein 17 (220233_at), score: 0.63
FKBPLFK506 binding protein like (219187_at), score: -0.68
FLJ12529pre-mRNA cleavage factor I, 59 kDa subunit (217866_at), score: 0.77
FOXK2forkhead box K2 (203064_s_at), score: 0.97
GATCglutamyl-tRNA(Gln) amidotransferase, subunit C homolog (bacterial) (214711_at), score: -0.7
GMCL1germ cell-less homolog 1 (Drosophila) (218458_at), score: -0.67
GOLPH3golgi phosphoprotein 3 (coat-protein) (217803_at), score: 1
GP1BAglycoprotein Ib (platelet), alpha polypeptide (207389_at), score: -0.84
GP1BBglycoprotein Ib (platelet), beta polypeptide (206655_s_at), score: 0.72
GPR107G protein-coupled receptor 107 (211979_at), score: 0.77
HIST1H2BIhistone cluster 1, H2bi (208523_x_at), score: -0.69
HSD17B6hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse) (37512_at), score: -0.79
HSPA12Aheat shock 70kDa protein 12A (214434_at), score: 0.74
IDUAiduronidase, alpha-L- (205059_s_at), score: 0.68
IL18R1interleukin 18 receptor 1 (206618_at), score: 0.67
KATNB1katanin p80 (WD repeat containing) subunit B 1 (203162_s_at), score: -0.71
KCNN2potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 (220116_at), score: -0.77
KCTD13potassium channel tetramerisation domain containing 13 (45653_at), score: 0.63
KIAA0317KIAA0317 (202128_at), score: 0.69
KIAA1009KIAA1009 (206005_s_at), score: -0.79
KIAA1305KIAA1305 (220911_s_at), score: 0.72
KPNA6karyopherin alpha 6 (importin alpha 7) (212101_at), score: 0.63
LOC100133105hypothetical protein LOC100133105 (214237_x_at), score: -0.85
LRDDleucine-rich repeats and death domain containing (221640_s_at), score: 0.67
MAPKAPK3mitogen-activated protein kinase-activated protein kinase 3 (202788_at), score: 0.7
MAST4microtubule associated serine/threonine kinase family member 4 (40016_g_at), score: 0.89
MBTPS2membrane-bound transcription factor peptidase, site 2 (206473_at), score: -0.79
MC4Rmelanocortin 4 receptor (221467_at), score: -0.84
MCTP1multiple C2 domains, transmembrane 1 (220122_at), score: 0.72
MICAL3microtubule associated monoxygenase, calponin and LIM domain containing 3 (212715_s_at), score: 0.65
MINK1misshapen-like kinase 1 (zebrafish) (214246_x_at), score: 0.64
MLL4myeloid/lymphoid or mixed-lineage leukemia 4 (203419_at), score: 0.7
MRPL2mitochondrial ribosomal protein L2 (218887_at), score: 0.66
MUL1mitochondrial E3 ubiquitin ligase 1 (218246_at), score: 0.63
NAALAD2N-acetylated alpha-linked acidic dipeptidase 2 (222161_at), score: 0.73
NCKAP1NCK-associated protein 1 (217465_at), score: -0.8
NEFMneurofilament, medium polypeptide (205113_at), score: -0.7
NENFneuron derived neurotrophic factor (218407_x_at), score: 0.64
NFATC4nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 (205897_at), score: 0.63
NUDT11nudix (nucleoside diphosphate linked moiety X)-type motif 11 (219855_at), score: 0.71
OR7E156Polfactory receptor, family 7, subfamily E, member 156 pseudogene (222327_x_at), score: -0.77
PAFAH1B2platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30kDa (210160_at), score: -0.69
PCDHGA1protocadherin gamma subfamily A, 1 (209079_x_at), score: 0.66
PDZRN4PDZ domain containing ring finger 4 (220595_at), score: 0.63
PIGLphosphatidylinositol glycan anchor biosynthesis, class L (213889_at), score: 0.73
PIP5K1Cphosphatidylinositol-4-phosphate 5-kinase, type I, gamma (212518_at), score: 0.66
PLAGL2pleiomorphic adenoma gene-like 2 (202925_s_at), score: 0.69
PMS2PMS2 postmeiotic segregation increased 2 (S. cerevisiae) (209805_at), score: -0.69
POLSpolymerase (DNA directed) sigma (202466_at), score: 0.64
POM121POM121 membrane glycoprotein (rat) (212178_s_at), score: 0.72
PTPN9protein tyrosine phosphatase, non-receptor type 9 (202958_at), score: 0.68
RAB22ARAB22A, member RAS oncogene family (218360_at), score: 0.8
RAD54L2RAD54-like 2 (S. cerevisiae) (213205_s_at), score: 0.91
RBBP9retinoblastoma binding protein 9 (221440_s_at), score: -0.79
REREarginine-glutamic acid dipeptide (RE) repeats (200940_s_at), score: 0.82
RNF220ring finger protein 220 (219988_s_at), score: 0.65
RPL18AP6ribosomal protein L18a pseudogene 6 (216383_at), score: -0.76
RPS17P5ribosomal protein S17 pseudogene 5 (216348_at), score: -0.77
RSAD1radical S-adenosyl methionine domain containing 1 (218307_at), score: 0.7
SCAMP4secretory carrier membrane protein 4 (213244_at), score: 0.67
SF1splicing factor 1 (208313_s_at), score: 0.65
SHQ1SHQ1 homolog (S. cerevisiae) (63009_at), score: 0.64
SIN3BSIN3 homolog B, transcription regulator (yeast) (209352_s_at), score: 0.68
SIPA1L3signal-induced proliferation-associated 1 like 3 (213600_at), score: 0.65
SIRT6sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) (219613_s_at), score: 0.87
SMG7Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans) (201794_s_at), score: 0.81
SNX27sorting nexin family member 27 (221006_s_at), score: 0.7
SOLHsmall optic lobes homolog (Drosophila) (204275_at), score: 0.79
STAU1staufen, RNA binding protein, homolog 1 (Drosophila) (207320_x_at), score: 0.67
TAPBPTAP binding protein (tapasin) (208829_at), score: 0.75
TBC1D2BTBC1 domain family, member 2B (212796_s_at), score: 0.68
TBX3T-box 3 (219682_s_at), score: 0.65
TLE6transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila) (222219_s_at), score: -0.69
TMED7transmembrane emp24 protein transport domain containing 7 (209404_s_at), score: -0.69
TMEM149transmembrane protein 149 (219690_at), score: -0.91
TOP3Atopoisomerase (DNA) III alpha (214300_s_at), score: -0.96
TSKUtsukushin (218245_at), score: 0.85
TTLL7tubulin tyrosine ligase-like family, member 7 (219882_at), score: -0.69
TXLNAtaxilin alpha (212300_at), score: 0.73
USF2upstream transcription factor 2, c-fos interacting (202152_x_at), score: 0.63
VAV3vav 3 guanine nucleotide exchange factor (218807_at), score: 0.65
VPS37Bvacuolar protein sorting 37 homolog B (S. cerevisiae) (221704_s_at), score: 0.77
WDR6WD repeat domain 6 (217734_s_at), score: 0.85
XAB2XPA binding protein 2 (218110_at), score: 0.71
YES1v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 (202932_at), score: 0.63
YPEL1yippee-like 1 (Drosophila) (206063_x_at), score: -0.75
ZDHHC14zinc finger, DHHC-type containing 14 (219247_s_at), score: -0.91
ZNF580zinc finger protein 580 (220748_s_at), score: 0.68
Non-Entrez genes
Unknown, score:
HELP
Conditions in the module, given in the same order as on the expression
plot above. Red color means over-expression, green under-expression in
the given condition.
The barplot below shows the condition (sample) scores. A separate bar
is shown for each sample, its height is the corresponding score of the
sample in the module. The red and green numbers on the bars are the
sample scores expressed in percents, i.e. 100% is 1.0.
The red and green lines show the module thresholds, samples above
the red line and below the green line are included in the module.
The different experiments that were part of the study, are separated
by dashed vertical lines.
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| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| E-TABM-263-raw-cel-1515485751.cel | 6 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485771.cel | 7 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486431.cel | 40 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486091.cel | 23 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486031.cel | 20 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
