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Module #758, TG: 2.6, TC: 1.6, 105 probes, 105 Entrez genes, 11 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:0042990 | 2.111e-02 | 0.1354 | 3
NF1, NFKBIA, SMAD3 | 13 | regulation of transcription factor import into nucleus |
| GO:0042991 | 2.111e-02 | 0.1354 | 3
NF1, NFKBIA, SMAD3 | 13 | transcription factor import into nucleus |
| GO:0045110 | 2.274e-02 | 0.03125 | 2
NEFL, NEFM | 3 | intermediate filament bundle assembly |
| GO:0051239 | 2.842e-02 | 3.333 | 11
ADORA2B, DMPK, EGF, GHR, NEFM, NF1, NFKBIA, PLAU, SMAD3, TICAM2, TP53 | 320 | regulation of multicellular organismal process |
| GO:0043525 | 3.704e-02 | 0.04167 | 2
NF1, TP53 | 4 | positive regulation of neuron apoptosis |
| GO:0060052 | 3.704e-02 | 0.04167 | 2
NEFL, NEFM | 4 | neurofilament cytoskeleton organization |
| GO:0043405 | 3.849e-02 | 0.7083 | 5
ADORA2B, EGF, GHR, NF1, PAK1 | 68 | regulation of MAP kinase activity |
| GO:0051223 | 4.670e-02 | 0.4375 | 4
EGF, NF1, NFKBIA, SMAD3 | 42 | regulation of protein transport |
| GO:0070201 | 4.670e-02 | 0.4375 | 4
EGF, NF1, NFKBIA, SMAD3 | 42 | regulation of establishment of protein 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:0005883 | 1.044e-02 | 0.03254 | 2
NEFL, NEFM | 3 | neurofilament |
| GO:0060053 | 1.882e-02 | 0.04339 | 2
NEFL, NEFM | 4 | neurofilament cytoskeleton |
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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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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
ACSL4acyl-CoA synthetase long-chain family member 4 (202422_s_at), score: 0.7
ACTR3BARP3 actin-related protein 3 homolog B (yeast) (218868_at), score: 0.8
ADARadenosine deaminase, RNA-specific (201786_s_at), score: -0.65
ADORA2Badenosine A2b receptor (205891_at), score: -0.68
AIM1absent in melanoma 1 (212543_at), score: -0.74
ALDH1L1aldehyde dehydrogenase 1 family, member L1 (215798_at), score: 0.68
ANXA10annexin A10 (210143_at), score: 0.67
ATP2C1ATPase, Ca++ transporting, type 2C, member 1 (211137_s_at), score: 0.71
BAT2HLA-B associated transcript 2 (212081_x_at), score: -0.7
C14orf45chromosome 14 open reading frame 45 (220173_at), score: 0.71
C20orf117chromosome 20 open reading frame 117 (207711_at), score: -0.66
C4orf43chromosome 4 open reading frame 43 (218513_at), score: 0.76
CALB2calbindin 2 (205428_s_at), score: 0.82
CASC3cancer susceptibility candidate 3 (207842_s_at), score: -0.69
CDC25Bcell division cycle 25 homolog B (S. pombe) (201853_s_at), score: -0.71
CDC2L6cell division cycle 2-like 6 (CDK8-like) (212899_at), score: -0.67
CDC42BPBCDC42 binding protein kinase beta (DMPK-like) (217849_s_at), score: -0.68
CDC42EP4CDC42 effector protein (Rho GTPase binding) 4 (214721_x_at), score: -0.8
CICcapicua homolog (Drosophila) (212784_at), score: -0.72
CITcitron (rho-interacting, serine/threonine kinase 21) (212801_at), score: -0.71
CNOT3CCR4-NOT transcription complex, subunit 3 (203239_s_at), score: -0.72
CRTC3CREB regulated transcription coactivator 3 (218648_at), score: -0.85
CScitrate synthase (208660_at), score: -0.68
DENND5BDENN/MADD domain containing 5B (215058_at), score: 0.69
DMPKdystrophia myotonica-protein kinase (37996_s_at), score: -0.66
DNAJB9DnaJ (Hsp40) homolog, subfamily B, member 9 (202843_at), score: 0.9
DNAJC6DnaJ (Hsp40) homolog, subfamily C, member 6 (204720_s_at), score: 0.7
EDEM1ER degradation enhancer, mannosidase alpha-like 1 (203279_at), score: 0.74
EGFepidermal growth factor (beta-urogastrone) (206254_at), score: 0.71
EPHA4EPH receptor A4 (206114_at), score: 0.67
FAM18Bfamily with sequence similarity 18, member B (218446_s_at), score: 0.71
FBXL14F-box and leucine-rich repeat protein 14 (213145_at), score: -0.82
FOXC2forkhead box C2 (MFH-1, mesenchyme forkhead 1) (214520_at), score: -0.7
FOXK2forkhead box K2 (203064_s_at), score: -0.71
GFOD1glucose-fructose oxidoreductase domain containing 1 (219821_s_at), score: 0.86
GHRgrowth hormone receptor (205498_at), score: 0.7
GK3Pglycerol kinase 3 pseudogene (215966_x_at), score: 0.81
GMCL1germ cell-less homolog 1 (Drosophila) (218458_at), score: 0.69
GMPRguanosine monophosphate reductase (204187_at), score: -0.69
H1FXH1 histone family, member X (204805_s_at), score: -0.76
HDGFhepatoma-derived growth factor (high-mobility group protein 1-like) (200896_x_at), score: -0.68
HMGA1high mobility group AT-hook 1 (210457_x_at), score: -0.68
HSD17B6hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse) (37512_at), score: 0.83
HSPA12Aheat shock 70kDa protein 12A (214434_at), score: -0.7
ITGA1integrin, alpha 1 (214660_at), score: 0.7
JUPjunction plakoglobin (201015_s_at), score: -0.73
KAL1Kallmann syndrome 1 sequence (205206_at), score: 1
KLHL23kelch-like 23 (Drosophila) (213610_s_at), score: 0.71
LOC391132similar to hCG2041276 (216177_at), score: 0.67
LOC440434hypothetical protein FLJ11822 (215090_x_at), score: -0.67
LRDDleucine-rich repeats and death domain containing (221640_s_at), score: -0.68
LRP8low density lipoprotein receptor-related protein 8, apolipoprotein e receptor (205282_at), score: 0.74
MDM2Mdm2 p53 binding protein homolog (mouse) (205386_s_at), score: -0.65
MFAP3Lmicrofibrillar-associated protein 3-like (205442_at), score: 0.77
NDPNorrie disease (pseudoglioma) (206022_at), score: -0.79
NEFLneurofilament, light polypeptide (221805_at), score: 0.69
NEFMneurofilament, medium polypeptide (205113_at), score: 0.98
NF1neurofibromin 1 (211094_s_at), score: -0.71
NFKBIAnuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (201502_s_at), score: -0.65
NOX4NADPH oxidase 4 (219773_at), score: 0.69
NPIPnuclear pore complex interacting protein (204538_x_at), score: -0.66
OAS32'-5'-oligoadenylate synthetase 3, 100kDa (218400_at), score: -0.68
OLFML2Bolfactomedin-like 2B (213125_at), score: -0.94
OLR1oxidized low density lipoprotein (lectin-like) receptor 1 (210004_at), score: 0.71
OPCMLopioid binding protein/cell adhesion molecule-like (214111_at), score: 0.75
OSTM1osteopetrosis associated transmembrane protein 1 (218196_at), score: 0.73
P2RY5purinergic receptor P2Y, G-protein coupled, 5 (218589_at), score: -0.66
PAK1p21 protein (Cdc42/Rac)-activated kinase 1 (209615_s_at), score: -0.69
PCDH9protocadherin 9 (219737_s_at), score: 0.95
PDE5Aphosphodiesterase 5A, cGMP-specific (206757_at), score: -0.79
PLAUplasminogen activator, urokinase (211668_s_at), score: -0.66
PLK1polo-like kinase 1 (Drosophila) (202240_at), score: -0.69
PRMT3protein arginine methyltransferase 3 (213320_at), score: 0.81
RAB1ARAB1A, member RAS oncogene family (213440_at), score: 0.77
REREarginine-glutamic acid dipeptide (RE) repeats (200940_s_at), score: -0.81
RFX5regulatory factor X, 5 (influences HLA class II expression) (202963_at), score: -0.65
RNF220ring finger protein 220 (219988_s_at), score: -0.73
RPL18AP6ribosomal protein L18a pseudogene 6 (216383_at), score: 0.76
RPS17P5ribosomal protein S17 pseudogene 5 (216348_at), score: 0.68
RRP15ribosomal RNA processing 15 homolog (S. cerevisiae) (219037_at), score: 0.68
SAP30LSAP30-like (219129_s_at), score: -0.77
SAV1salvador homolog 1 (Drosophila) (218276_s_at), score: -0.68
SCAMP4secretory carrier membrane protein 4 (213244_at), score: -0.8
SDPRserum deprivation response (phosphatidylserine binding protein) (218711_s_at), score: -0.65
SERPINB9serpin peptidase inhibitor, clade B (ovalbumin), member 9 (209723_at), score: -0.67
SF1splicing factor 1 (208313_s_at), score: -0.77
SLC33A1solute carrier family 33 (acetyl-CoA transporter), member 1 (203165_s_at), score: 0.74
SLC43A3solute carrier family 43, member 3 (213113_s_at), score: -0.68
SLC4A7solute carrier family 4, sodium bicarbonate cotransporter, member 7 (209884_s_at), score: 0.74
SMAD3SMAD family member 3 (218284_at), score: -0.73
STIM1stromal interaction molecule 1 (202764_at), score: -0.71
SULT1B1sulfotransferase family, cytosolic, 1B, member 1 (207601_at), score: 0.67
SYNE1spectrin repeat containing, nuclear envelope 1 (209447_at), score: 0.74
TGDSTDP-glucose 4,6-dehydratase (208249_s_at), score: 0.67
THSD7Athrombospondin, type I, domain containing 7A (214920_at), score: -0.68
TICAM2toll-like receptor adaptor molecule 2 (214658_at), score: 0.77
TLE4transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) (204872_at), score: 0.69
TMSB15Bthymosin beta 15B (214051_at), score: -0.66
TP53tumor protein p53 (201746_at), score: -0.75
TRIM21tripartite motif-containing 21 (204804_at), score: -0.69
TRMT2ATRM2 tRNA methyltransferase 2 homolog A (S. cerevisiae) (91617_at), score: 0.69
VEGFBvascular endothelial growth factor B (203683_s_at), score: -0.66
WDR6WD repeat domain 6 (217734_s_at), score: -0.8
YES1v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 (202932_at), score: -0.76
ZDHHC7zinc finger, DHHC-type containing 7 (218606_at), score: -0.72
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-1515486211.cel | 29 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485871.cel | 12 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485691.cel | 3 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485711.cel | 4 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485751.cel | 6 | 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-1515485671.cel | 2 | 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-1515485811.cel | 9 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485891.cel | 13 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515486371.cel | 37 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
