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Module #364, TG: 2.2, TC: 2.6, 123 probes, 123 Entrez genes, 4 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:0006106 | 2.616e-02 | 0.04437 | 2 FH, GOT1 | 2 | fumarate metabolic process |
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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:0044429 | 1.999e-02 | 4.314 | 12 AARS2, AIFM2, BCKDHB, FH, GARS, GATM, HADHA, ME2, NDUFA6, RNF144B, SUPV3L1, TIMM10 | 191 | mitochondrial part |
GO:0005739 | 2.081e-02 | 9.643 | 20 AARS2, AIFM2, BCKDHB, C6orf57, FAM82B, FH, GARS, GATM, HADHA, HEBP1, ME2, MRPL19, MRPL50, MRPS30, NDUFA6, PACS2, RNF144B, RTN4IP1, SUPV3L1, TIMM10 | 427 | mitochondrion |
GO:0005759 | 2.207e-02 | 1.671 | 7 AARS2, BCKDHB, FH, GARS, HADHA, ME2, SUPV3L1 | 74 | mitochondrial matrix |
GO:0031980 | 2.207e-02 | 1.671 | 7 AARS2, BCKDHB, FH, GARS, HADHA, ME2, SUPV3L1 | 74 | mitochondrial lumen |
GO:0045239 | 2.493e-02 | 0.06775 | 2 BCKDHB, FH | 3 | tricarboxylic acid cycle enzyme complex |
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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.
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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.
Text color indicates correlation and anti-correlation: genes of the
same color are correlated, both move up or down in the module samples
(listed below). Genes of different color are anti-correlated, they
have opposite behavior in the module samples.
Note, that text color of the individual genes should be interpreted
together with the coloring of the samples below. For
red samples,
red genes have a higher expression
(compared to the average gene expression level),
green genes have a lower
expression.
Green samples have opposite
behavior, in these red genes have a
lower expression, green genes
have a higher expression.
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
AARS2alanyl-tRNA synthetase 2, mitochondrial (putative) (ENSG00000124608), score: 0.69
ABHD12abhydrolase domain containing 12 (ENSG00000100997), score: -0.59
ABHD6abhydrolase domain containing 6 (ENSG00000163686), score: -0.59
ACER2alkaline ceramidase 2 (ENSG00000177076), score: 0.45
ACER3alkaline ceramidase 3 (ENSG00000078124), score: 0.57
ACTL6Aactin-like 6A (ENSG00000136518), score: 0.49
AIFM2apoptosis-inducing factor, mitochondrion-associated, 2 (ENSG00000042286), score: 0.57
AMPD1adenosine monophosphate deaminase 1 (ENSG00000116748), score: 0.67
AP4E1adaptor-related protein complex 4, epsilon 1 subunit (ENSG00000081014), score: 0.53
APBB2amyloid beta (A4) precursor protein-binding, family B, member 2 (ENSG00000163697), score: -0.51
ARFGAP3ADP-ribosylation factor GTPase activating protein 3 (ENSG00000242247), score: 0.44
ARHGEF38Rho guanine nucleotide exchange factor (GEF) 38 (ENSG00000138784), score: 0.62
ARL14ADP-ribosylation factor-like 14 (ENSG00000179674), score: 1
ARL5BADP-ribosylation factor-like 5B (ENSG00000165997), score: 0.59
ATG16L1ATG16 autophagy related 16-like 1 (S. cerevisiae) (ENSG00000085978), score: 0.45
ATG4AATG4 autophagy related 4 homolog A (S. cerevisiae) (ENSG00000101844), score: 0.58
ATMINATM interactor (ENSG00000166454), score: -0.58
B4GALT5UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 (ENSG00000158470), score: -0.53
BCKDHBbranched chain keto acid dehydrogenase E1, beta polypeptide (ENSG00000083123), score: 0.49
BLMHbleomycin hydrolase (ENSG00000108578), score: 0.43
C1orf123chromosome 1 open reading frame 123 (ENSG00000162384), score: 0.46
C6orf162chromosome 6 open reading frame 162 (ENSG00000111850), score: 0.5
C6orf57chromosome 6 open reading frame 57 (ENSG00000154079), score: 0.45
C7orf30chromosome 7 open reading frame 30 (ENSG00000156928), score: 0.5
CIAO1cytosolic iron-sulfur protein assembly 1 (ENSG00000144021), score: 0.51
CNGA2cyclic nucleotide gated channel alpha 2 (ENSG00000183862), score: 0.47
CREB3L3cAMP responsive element binding protein 3-like 3 (ENSG00000060566), score: 0.53
CYSLTR1cysteinyl leukotriene receptor 1 (ENSG00000173198), score: 0.52
CYTH1cytohesin 1 (ENSG00000108669), score: -0.48
DCTN5dynactin 5 (p25) (ENSG00000166847), score: -0.55
DDX27DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 (ENSG00000124228), score: 0.44
DPH5DPH5 homolog (S. cerevisiae) (ENSG00000117543), score: 0.48
EEA1early endosome antigen 1 (ENSG00000102189), score: 0.6
EIF3Deukaryotic translation initiation factor 3, subunit D (ENSG00000100353), score: 0.55
EIF3Meukaryotic translation initiation factor 3, subunit M (ENSG00000149100), score: 0.54
F8coagulation factor VIII, procoagulant component (ENSG00000185010), score: 0.56
FAM3Dfamily with sequence similarity 3, member D (ENSG00000198643), score: 0.48
FAM82Bfamily with sequence similarity 82, member B (ENSG00000176623), score: 0.63
FGF6fibroblast growth factor 6 (ENSG00000111241), score: 0.55
FHfumarate hydratase (ENSG00000091483), score: 0.48
FZD2frizzled homolog 2 (Drosophila) (ENSG00000180340), score: 0.56
GARSglycyl-tRNA synthetase (ENSG00000106105), score: 0.48
GATMglycine amidinotransferase (L-arginine:glycine amidinotransferase) (ENSG00000171766), score: -0.54
GCNT7glucosaminyl (N-acetyl) transferase family member 7 (ENSG00000124091), score: 0.65
GOT1glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1) (ENSG00000120053), score: 0.44
GPX7glutathione peroxidase 7 (ENSG00000116157), score: 0.51
GTF2E1general transcription factor IIE, polypeptide 1, alpha 56kDa (ENSG00000153767), score: 0.49
GTPBP8GTP-binding protein 8 (putative) (ENSG00000163607), score: 0.64
HADHAhydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit (ENSG00000084754), score: 0.46
HEBP1heme binding protein 1 (ENSG00000013583), score: 0.53
HMGXB4HMG box domain containing 4 (ENSG00000100281), score: 0.49
ICOSLGinducible T-cell co-stimulator ligand (ENSG00000160223), score: 0.46
IKZF3IKAROS family zinc finger 3 (Aiolos) (ENSG00000161405), score: 0.46
KIAA0090KIAA0090 (ENSG00000127463), score: 0.51
KIAA0664KIAA0664 (ENSG00000132361), score: 0.48
KIAA1432KIAA1432 (ENSG00000107036), score: 0.48
KLHL5kelch-like 5 (Drosophila) (ENSG00000109790), score: -0.67
LRP11low density lipoprotein receptor-related protein 11 (ENSG00000120256), score: -0.53
LRP3low density lipoprotein receptor-related protein 3 (ENSG00000130881), score: -0.61
LY75lymphocyte antigen 75 (ENSG00000054219), score: 0.55
ME2malic enzyme 2, NAD(+)-dependent, mitochondrial (ENSG00000082212), score: -0.51
MRPL19mitochondrial ribosomal protein L19 (ENSG00000115364), score: 0.47
MRPL50mitochondrial ribosomal protein L50 (ENSG00000136897), score: 0.51
MRPS30mitochondrial ribosomal protein S30 (ENSG00000112996), score: 0.44
MTAPmethylthioadenosine phosphorylase (ENSG00000099810), score: 0.5
NDUFA6NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa (ENSG00000184983), score: 0.48
NIPA1non imprinted in Prader-Willi/Angelman syndrome 1 (ENSG00000170113), score: -0.48
NOP58NOP58 ribonucleoprotein homolog (yeast) (ENSG00000055044), score: 0.46
NRBF2nuclear receptor binding factor 2 (ENSG00000148572), score: 0.45
OSBPL2oxysterol binding protein-like 2 (ENSG00000130703), score: -0.58
OXSR1oxidative-stress responsive 1 (ENSG00000172939), score: 0.65
PACS2phosphofurin acidic cluster sorting protein 2 (ENSG00000179364), score: -0.5
PCGF3polycomb group ring finger 3 (ENSG00000185619), score: -0.48
PEX7peroxisomal biogenesis factor 7 (ENSG00000112357), score: 0.47
PHF5APHD finger protein 5A (ENSG00000100410), score: 0.47
PHKA2phosphorylase kinase, alpha 2 (liver) (ENSG00000044446), score: 0.53
PIGLphosphatidylinositol glycan anchor biosynthesis, class L (ENSG00000108474), score: 0.44
PITPNAphosphatidylinositol transfer protein, alpha (ENSG00000174238), score: -0.51
PLXNB1plexin B1 (ENSG00000164050), score: -0.5
PM20D1peptidase M20 domain containing 1 (ENSG00000162877), score: 0.46
PM20D2peptidase M20 domain containing 2 (ENSG00000146281), score: 0.44
PODNpodocan (ENSG00000174348), score: 0.49
PPEF2protein phosphatase, EF-hand calcium binding domain 2 (ENSG00000156194), score: 0.79
PTP4A2protein tyrosine phosphatase type IVA, member 2 (ENSG00000184007), score: 0.45
PYCRLpyrroline-5-carboxylate reductase-like (ENSG00000104524), score: 0.44
QSOX1quiescin Q6 sulfhydryl oxidase 1 (ENSG00000116260), score: -0.65
RAI1retinoic acid induced 1 (ENSG00000108557), score: -0.5
RGS18regulator of G-protein signaling 18 (ENSG00000150681), score: 0.45
RNF144Aring finger protein 144A (ENSG00000151692), score: -0.54
RNF144Bring finger protein 144B (ENSG00000137393), score: 0.6
RNF145ring finger protein 145 (ENSG00000145860), score: -0.56
RTN4IP1reticulon 4 interacting protein 1 (ENSG00000130347), score: 0.49
SGSM2small G protein signaling modulator 2 (ENSG00000141258), score: -0.55
SIKE1suppressor of IKBKE 1 (ENSG00000052723), score: 0.54
SLC22A3solute carrier family 22 (extraneuronal monoamine transporter), member 3 (ENSG00000146477), score: 0.66
SLC46A1solute carrier family 46 (folate transporter), member 1 (ENSG00000076351), score: 0.48
SLC7A2solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 (ENSG00000003989), score: 0.51
SNRNP48small nuclear ribonucleoprotein 48kDa (U11/U12) (ENSG00000168566), score: 0.44
SNX24sorting nexin 24 (ENSG00000064652), score: 0.46
SPIRE1spire homolog 1 (Drosophila) (ENSG00000134278), score: -0.53
STK39serine threonine kinase 39 (ENSG00000198648), score: -0.5
SUPV3L1suppressor of var1, 3-like 1 (S. cerevisiae) (ENSG00000156502), score: 0.51
TALDO1transaldolase 1 (ENSG00000177156), score: 0.49
TIMM10translocase of inner mitochondrial membrane 10 homolog (yeast) (ENSG00000134809), score: 0.61
TMCO3transmembrane and coiled-coil domains 3 (ENSG00000150403), score: -0.53
TMEM9transmembrane protein 9 (ENSG00000116857), score: -0.58
TNFRSF21tumor necrosis factor receptor superfamily, member 21 (ENSG00000146072), score: -0.54
TNMDtenomodulin (ENSG00000000005), score: 0.5
TOR1Btorsin family 1, member B (torsin B) (ENSG00000136816), score: 0.44
TP53BP1tumor protein p53 binding protein 1 (ENSG00000067369), score: -0.63
TRAPPC3trafficking protein particle complex 3 (ENSG00000054116), score: -0.53
TRDMT1tRNA aspartic acid methyltransferase 1 (ENSG00000107614), score: 0.45
TRNAU1APtRNA selenocysteine 1 associated protein 1 (ENSG00000180098), score: 0.54
TRRAPtransformation/transcription domain-associated protein (ENSG00000196367), score: -0.55
TSG101tumor susceptibility gene 101 (ENSG00000074319), score: 0.48
TTF2transcription termination factor, RNA polymerase II (ENSG00000116830), score: 0.7
UTP15UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae) (ENSG00000164338), score: 0.5
WDFY2WD repeat and FYVE domain containing 2 (ENSG00000139668), score: 0.63
WDR37WD repeat domain 37 (ENSG00000047056), score: -0.55
WDR43WD repeat domain 43 (ENSG00000163811), score: 0.44
XCR1chemokine (C motif) receptor 1 (ENSG00000173578), score: 0.48
YIPF1Yip1 domain family, member 1 (ENSG00000058799), score: 0.58
YTHDC2YTH domain containing 2 (ENSG00000047188), score: -0.48
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 height of each bar corresponds to the weighted
mean expression of the module genes. The weights are the gene scores
of the module and they are positive for the genes listed in
red above and they are negative for
the genes that are listed in
green.
Bars going up correspond to samples listed in
red (the ones that are different
enough to included in the module). In these samples
the red module genes are highly
expressed, and the green
module genes are lowly expressed. The behavior of the genes is the
opposite for bars going down.
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 species and tissues that were part of the study, are separated
by dashed vertical lines.
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Id | species | tissue | sex | individual |
oan_ht_f_ca1 | oan | ht | f | _ |
oan_ht_m_ca1 | oan | ht | m | _ |
mdo_lv_f_ca1 | mdo | lv | f | _ |
mdo_lv_m_ca1 | mdo | lv | m | _ |
© 2008-2010 Computational Biology Group, Department of Medical Genetics,
University of Lausanne, Switzerland