Previous module |
Next module
Module #658, TG: 2.8, TC: 2, 126 probes, 126 Entrez genes, 3 conditions
HELP
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).
— Click on the Help button again to close this help window.
Under-expression is coded with green,
over-expression with red color.
Help |
Hide |
Top
Help |
Show |
Top
The GO tree — Biological processes
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
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.
Help |
Hide |
Top
Help |
Show |
Top
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.
Help |
Hide |
Top
Help |
Show |
Top
GO BP test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
GO CC test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0030173 | 1.072e-02 | 0.3423 | 4
A4GALT, MAN1C1, MFNG, ST8SIA3 | 25 | integral to Golgi membrane |
| GO:0031301 | 1.499e-02 | 1.013 | 6
A4GALT, ASPHD1, MAN1C1, MFNG, ST8SIA3, STIM1 | 74 | integral to organelle membrane |
| GO:0031228 | 1.574e-02 | 0.3834 | 4
A4GALT, MAN1C1, MFNG, ST8SIA3 | 28 | intrinsic to Golgi membrane |
| GO:0005576 | 2.000e-02 | 9.216 | 20
ADAMTS7, APOC4, CEACAM1, CFI, CLCA2, DSPP, GAST, HGF, IGHG1, IL23A, IL9R, INHA, LILRA5, MFNG, MUC5AC, NDP, RLN1, SEPP1, SIGLEC1, WFDC8 | 673 | extracellular region |
| GO:0031300 | 3.499e-02 | 1.232 | 6
A4GALT, ASPHD1, MAN1C1, MFNG, ST8SIA3, STIM1 | 90 | intrinsic to organelle membrane |
Help |
Hide |
Top
Help |
Show |
Top
GO MF test for over-representation
HELP
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.
| Id | Pvalue | ExpCount | Count | Size | Term |
| GO:0005078 | 2.029e-02 | 0.02754 | 2
MAPK8IP1, MAPK8IP2 | 2 | MAP-kinase scaffold activity |
| GO:0030159 | 4.138e-02 | 0.1652 | 3
MAPK8IP1, MAPK8IP2, SHANK2 | 12 | receptor signaling complex scaffold activity |
Help |
Hide |
Top
Help |
Show |
Top
KEGG Pathway test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
miRNA test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
Help |
Hide |
Top
Help |
Show |
Top
Chromosome test for over-representation
HELP
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.
— Click on the Help button again to close this help window.
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.
— Click on the Help button again to close this help window.
Entrez genes
A4GALTalpha 1,4-galactosyltransferase (219488_at), score: 0.51
ABCA7ATP-binding cassette, sub-family A (ABC1), member 7 (219577_s_at), score: 0.84
ABCA8ATP-binding cassette, sub-family A (ABC1), member 8 (204719_at), score: -0.61
ABLIM1actin binding LIM protein 1 (200965_s_at), score: -0.59
ACSS3acyl-CoA synthetase short-chain family member 3 (219616_at), score: -0.57
ADAMTS7ADAM metallopeptidase with thrombospondin type 1 motif, 7 (220705_s_at), score: 0.77
ADORA1adenosine A1 receptor (216220_s_at), score: 0.6
AGBL2ATP/GTP binding protein-like 2 (220390_at), score: 0.57
AHCYL2S-adenosylhomocysteine hydrolase-like 2 (212814_at), score: -0.6
APOC4apolipoprotein C-IV (206738_at), score: 0.62
ASPHD1aspartate beta-hydroxylase domain containing 1 (214993_at), score: 0.6
ATP8B2ATPase, class I, type 8B, member 2 (216873_s_at), score: 0.56
BCAMbasal cell adhesion molecule (Lutheran blood group) (40093_at), score: 0.61
BIRC3baculoviral IAP repeat-containing 3 (210538_s_at), score: -0.7
C21orf2chromosome 21 open reading frame 2 (203996_s_at), score: 0.66
C9orf127chromosome 9 open reading frame 127 (207839_s_at), score: -0.55
CC2D1Acoiled-coil and C2 domain containing 1A (58994_at), score: 0.59
CCDC40coiled-coil domain containing 40 (220592_at), score: 0.73
CD79BCD79b molecule, immunoglobulin-associated beta (205297_s_at), score: 0.86
CDO1cysteine dioxygenase, type I (204154_at), score: -0.55
CEACAM1carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) (211883_x_at), score: 0.75
CEP164centrosomal protein 164kDa (204251_s_at), score: -0.68
CFIcomplement factor I (203854_at), score: -0.74
CHRNA6cholinergic receptor, nicotinic, alpha 6 (207568_at), score: 0.53
CLCA2chloride channel accessory 2 (206165_s_at), score: -0.58
CNNM3cyclin M3 (220739_s_at), score: -0.63
CYorf15Bchromosome Y open reading frame 15B (214131_at), score: 0.57
DLX4distal-less homeobox 4 (208216_at), score: 0.56
DMPKdystrophia myotonica-protein kinase (37996_s_at), score: -0.63
DSPPdentin sialophosphoprotein (221681_s_at), score: 0.55
EPHB4EPH receptor B4 (216680_s_at), score: 0.55
EPS8L1EPS8-like 1 (218778_x_at), score: 0.6
EXPH5exophilin 5 (214734_at), score: -0.7
FKBP10FK506 binding protein 10, 65 kDa (219249_s_at), score: 1
FOSL2FOS-like antigen 2 (218880_at), score: -0.58
FUZfuzzy homolog (Drosophila) (221187_s_at), score: 0.54
GASTgastrin (208138_at), score: 0.67
GATMglycine amidinotransferase (L-arginine:glycine amidinotransferase) (203178_at), score: -0.61
GBA3glucosidase, beta, acid 3 (cytosolic) (219954_s_at), score: 0.63
HAB1B1 for mucin (215778_x_at), score: 0.56
HGFhepatocyte growth factor (hepapoietin A; scatter factor) (209960_at), score: -0.59
HIPK2homeodomain interacting protein kinase 2 (219028_at), score: 0.62
HIST1H2AGhistone cluster 1, H2ag (207156_at), score: -0.59
HIST1H4Ghistone cluster 1, H4g (208551_at), score: 0.57
HPNhepsin (204934_s_at), score: 0.51
HSPA4Lheat shock 70kDa protein 4-like (205543_at), score: -0.76
HSPA6heat shock 70kDa protein 6 (HSP70B') (117_at), score: 0.69
ICAM2intercellular adhesion molecule 2 (204683_at), score: 0.54
IGHG1immunoglobulin heavy constant gamma 1 (G1m marker) (211693_at), score: 0.83
IL23Ainterleukin 23, alpha subunit p19 (211796_s_at), score: 0.58
IL9Rinterleukin 9 receptor (217212_s_at), score: 0.55
INAinternexin neuronal intermediate filament protein, alpha (204465_s_at), score: -0.84
INHAinhibin, alpha (210141_s_at), score: 0.66
IRF2interferon regulatory factor 2 (203275_at), score: -0.58
ITGALintegrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide) (213475_s_at), score: 0.69
JARID1Ajumonji, AT rich interactive domain 1A (215698_at), score: -0.62
KCTD15potassium channel tetramerisation domain containing 15 (218553_s_at), score: 0.55
KIAA0999KIAA0999 protein (204157_s_at), score: -0.55
KIAA1305KIAA1305 (220911_s_at), score: -0.6
KIF16Bkinesin family member 16B (219570_at), score: -0.6
KIF5Akinesin family member 5A (205318_at), score: -0.67
KRT24keratin 24 (220267_at), score: 0.57
KRT8P12keratin 8 pseudogene 12 (222060_at), score: 0.85
LILRA5leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 5 (215838_at), score: 0.66
LILRB3leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 (211133_x_at), score: 0.66
LILRB4leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4 (210152_at), score: 0.66
LOC100128919similar to HSPC157 (219865_at), score: -0.79
LOC388152hypothetical LOC388152 (220602_s_at), score: 0.56
LOC80054hypothetical LOC80054 (220465_at), score: 0.67
MAN1C1mannosidase, alpha, class 1C, member 1 (218918_at), score: -0.56
MAPK8IP1mitogen-activated protein kinase 8 interacting protein 1 (213013_at), score: 0.53
MAPK8IP2mitogen-activated protein kinase 8 interacting protein 2 (205050_s_at), score: 0.54
MFNGMFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase (204153_s_at), score: 0.71
MUC3Bmucin 3B, cell surface associated (214898_x_at), score: 0.79
MUC5ACmucin 5AC, oligomeric mucus/gel-forming (217182_at), score: 0.7
MYH15myosin, heavy chain 15 (215331_at), score: 0.52
MYO15Amyosin XVA (220288_at), score: 0.53
NDPNorrie disease (pseudoglioma) (206022_at), score: -0.64
NEBLnebulette (216882_s_at), score: 0.64
NEO1neogenin homolog 1 (chicken) (204321_at), score: -0.66
NPEPL1aminopeptidase-like 1 (89476_r_at), score: 0.52
OPRL1opiate receptor-like 1 (206564_at), score: 0.59
PHC1polyhomeotic homolog 1 (Drosophila) (218338_at), score: -0.65
PHF2PHD finger protein 2 (212726_at), score: -0.79
PIAS3protein inhibitor of activated STAT, 3 (203035_s_at), score: -0.67
PIPOXpipecolic acid oxidase (221605_s_at), score: 0.56
PIWIL1piwi-like 1 (Drosophila) (214868_at), score: 0.65
PLA2G4Cphospholipase A2, group IVC (cytosolic, calcium-independent) (209785_s_at), score: -0.56
PLXNB3plexin B3 (205957_at), score: 0.52
POM121L2POM121 membrane glycoprotein-like 2 (rat) (216582_at), score: 0.63
PTPN20Bprotein tyrosine phosphatase, non-receptor type 20B (215172_at), score: -0.64
PTPN6protein tyrosine phosphatase, non-receptor type 6 (206687_s_at), score: 0.55
RAB1ARAB1A, member RAS oncogene family (213440_at), score: 0.54
RBM12BRNA binding motif protein 12B (51228_at), score: -0.68
RBM38RNA binding motif protein 38 (212430_at), score: 0.79
RBM4BRNA binding motif protein 4B (209497_s_at), score: -0.66
RLN1relaxin 1 (211753_s_at), score: 0.69
RNF121ring finger protein 121 (219021_at), score: 0.52
ROS1c-ros oncogene 1 , receptor tyrosine kinase (207569_at), score: 0.63
SEPP1selenoprotein P, plasma, 1 (201427_s_at), score: -0.65
SEPT5septin 5 (209767_s_at), score: 0.58
SH2D3ASH2 domain containing 3A (222169_x_at), score: 0.56
SHANK2SH3 and multiple ankyrin repeat domains 2 (213307_at), score: -0.56
SIGLEC1sialic acid binding Ig-like lectin 1, sialoadhesin (44673_at), score: 0.6
SLC35F5solute carrier family 35, member F5 (220123_at), score: -0.55
SNAP25synaptosomal-associated protein, 25kDa (202508_s_at), score: -0.71
SPEF1sperm flagellar 1 (216119_s_at), score: 0.55
SSX3synovial sarcoma, X breakpoint 3 (215881_x_at), score: 0.54
ST8SIA3ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3 (208064_s_at), score: 0.75
STIM1stromal interaction molecule 1 (202764_at), score: -0.63
TAF15TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68kDa (202840_at), score: 0.67
TCP10t-complex 10 homolog (mouse) (207503_at), score: 0.69
TIAF1TGFB1-induced anti-apoptotic factor 1 (202039_at), score: -0.57
TMEM30Btransmembrane protein 30B (213285_at), score: -0.6
TMEM40transmembrane protein 40 (219503_s_at), score: 0.52
TMPRSS6transmembrane protease, serine 6 (214955_at), score: 0.8
TMSB4Ythymosin beta 4, Y-linked (206769_at), score: 0.55
TNK1tyrosine kinase, non-receptor, 1 (217149_x_at), score: 0.58
TRIM21tripartite motif-containing 21 (204804_at), score: -0.57
TSKStestis-specific serine kinase substrate (220545_s_at), score: 0.59
ULK1unc-51-like kinase 1 (C. elegans) (209333_at), score: -0.59
WFDC8WAP four-disulfide core domain 8 (215276_at), score: 0.56
YPEL1yippee-like 1 (Drosophila) (206063_x_at), score: 0.55
ZNF132zinc finger protein 132 (207402_at), score: -0.75
ZNF192zinc finger protein 192 (206579_at), score: -0.79
ZNF318zinc finger protein 318 (203521_s_at), score: -0.61
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.
— Click on the Help button again to close this help window.
| Id | sample | Experiment | ExpName | Array | Syndrome | Cell.line |
| E-TABM-263-raw-cel-1515486311.cel | 34 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485931.cel | 15 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
| E-TABM-263-raw-cel-1515485671.cel | 2 | 6 | Cycle | hgu133a2 | none | Cycle 1 |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland
