From da5ec1335f3704e87ac36b4d926131841f9abfb8 Mon Sep 17 00:00:00 2001 From: Thomas Rauter <93391936+Thomas-Rauter@users.noreply.github.com> Date: Wed, 25 Sep 2024 08:54:30 +0200 Subject: [PATCH] Rename report_clustered_hits_PTX_19_09_2024-13_47_08.html to report_clustered_hits_PTX.html --- report_clustered_hits_PTX.html | 1 + ...lustered_hits_PTX_19_09_2024-13_47_08.html | 332 ------------------ 2 files changed, 1 insertion(+), 332 deletions(-) create mode 100644 report_clustered_hits_PTX.html delete mode 100644 report_clustered_hits_PTX_19_09_2024-13_47_08.html diff --git a/report_clustered_hits_PTX.html b/report_clustered_hits_PTX.html new file mode 100644 index 0000000..d3f5a12 --- /dev/null +++ b/report_clustered_hits_PTX.html @@ -0,0 +1 @@ + diff --git a/report_clustered_hits_PTX_19_09_2024-13_47_08.html b/report_clustered_hits_PTX_19_09_2024-13_47_08.html deleted file mode 100644 index 3c493ae..0000000 --- a/report_clustered_hits_PTX_19_09_2024-13_47_08.html +++ /dev/null @@ -1,332 +0,0 @@ -clustered hits | time_effect

clustered hits | time_effect | Omics-Datatype: PTX | Date-Time: 20_09_2024-15_46_33


Note!

Clustering of features that show significant changes over time (= hits).
Clustering was done based on the min-max normalized shape of the spline.
For this, the spline parameters in the limma topTable are used to generate 1000 curve datapoints between 0 and 1. These datapoints are used for hierarchical clustering.
Right-click on any plot in this report to save it as a .svg (vector graphic) file!
If one level of the experiment is not shown, it means it has < 2 hits!

feature_name "formula": {annotation-column-x}_{annotation-column-y}_ ... :



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Report Info ℹ

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omics data type - :PTX
data description - :Proteomics data of CHO cells
data collection date - :February 2024
meta condition - :Phase
meta batch - :Reactor,
limma design - :~ 1 + Phase*X + Reactor
analyst name - :Thomas Rauter
contact info - :thomas.rauter@plus.ac.at
project name - :DGTX
method description - :NA
results summary - :NA
conclusions - :NA
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Downloads 📥

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data with annotation - : -
meta - : -
limma topTables - : -
Enrichr clustered genes - : -
Enrichr background - : -
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Table of Contents

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Exponential

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- Spline-type: Natural cubic spline
- DoF: 2
- Knots: NA
- Boundary-knots: NA -

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adj.p-value threshold: 0.050

Number of hits: 134

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Overall Clustering

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Min-max normalized individual and mean splines

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Z-Score of log2 Value Heatmap

Rows = features (labels on the right, cluster labels on the left), columns = timepoints; Blue = down, red = up, --> compared to the rest - of the row;
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Individual Significant Features (Hits) Splines

- Asterisks definition:
Adj. p-value < 0.05 --> *
Adj. p-value < 0.01 --> **
Adj. p-value < 0.001 --> ***
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Cluster 1 | Hits: 30

ASPSCR1 tether for SLC2A4, UBX domain containing
Plot
ATP synthase membrane subunit f
Plot
ATPase plasma membrane Ca2+ transporting 3
Plot
CCHC-type zinc finger nucleic acid binding protein
Plot
ER membrane protein complex subunit 3
Plot
LKAAEAR motif containing 1
Plot
UTP20 small subunit processome component
Plot
actin like 6A
Plot
actin related protein 3
Plot
acyl-CoA desaturase 1
Plot
adhesion G protein-coupled receptor F5
Plot
calcium release activated channel regulator 2A
Plot
chloride channel CLIC like 1
Plot
coiled-coil domain containing 60
Plot
crystallin beta A4
Plot
geranylgeranyl diphosphate synthase 1
Plot
immunoglobulin superfamily containing leucine rich repeat
Plot
membrane bound O-acyltransferase domain containing 4
Plot
pleckstrin homology and coiled-coil domain containing D1
Plot
protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1
Plot
regulator of G protein signaling 7
Plot
small integral membrane protein 41
Plot
solute carrier family 26 member 9
Plot
speedy protein E4
Plot
striatin
Plot
synoviolin 1
Plot
tRNA aspartic acid methyltransferase 1
Plot
ubiquitin conjugating enzyme E2 W
Plot
ubiquitin specific peptidase 19
Plot
zinc finger CCCH-type containing 14
Plot
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Cluster 2 | Hits: 46

1-acylglycerol-3-phosphate O-acyltransferase 2
Plot
AHNAK nucleoprotein 2
Plot
ATPase phospholipid transporting 10D (putative)
Plot
C-type lectin domain containing 16A
Plot
CLOCK interacting pacemaker
Plot
CTTNBP2 N-terminal like
Plot
DEAD-box helicase 27
Plot
DNA fragmentation factor subunit beta
Plot
DnaJ heat shock protein family (Hsp40) member B5
Plot
EPH receptor A1
Plot
GDNF family receptor alpha 2
Plot
NPC1 like intracellular cholesterol transporter 1
Plot
RNA polymerase III subunit B
Plot
SAP domain-containing ribonucleoprotein-like
Plot
SKI family transcriptional corepressor 1
Plot
STIL centriolar assembly protein
Plot
WD repeat containing, antisense to TP73
Plot
acid sensing ion channel subunit 2
Plot
afadin, adherens junction formation factor
Plot
ankyrin repeat and sterile alpha motif domain containing 1B
Plot
armadillo repeat-containing protein 7
Plot
cell division cycle associated 3
Plot
cofilin 1
Plot
coiled-coil domain containing 142
Plot
cytidine/uridine monophosphate kinase 1
Plot
family with sequence similarity 181 member A
Plot
glutathione S-transferase zeta 1
Plot
inhibitor of nuclear factor kappa B kinase subunit beta
Plot
leucine rich repeat containing 14B
Plot
lysine acetyltransferase 2A
Plot
poly(A) binding protein cytoplasmic 4 like
Plot
protein phosphatase 1 regulatory subunit 26
Plot
ribonucleic acid export 1
Plot
schwannomin-interacting protein 1
Plot
serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B
Plot
serotransferrin
Plot
small EDRK-rich factor 2
Plot
solute carrier family 35 member D3
Plot
spidroin-2-like
Plot
sterile alpha motif domain containing 12
Plot
structural maintenance of chromosomes 3
Plot
testis associated actin remodelling kinase 2
Plot
thioredoxin domain containing 16
Plot
ubiquitin conjugating enzyme E2 U
Plot
vesicle trafficking 1
Plot
zinc finger MIZ-type containing 2
Plot
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Cluster 3 | Hits: 15

ADP ribosylation factor like GTPase 1
Plot
Coenzyme A synthase
Plot
IQ motif containing G
Plot
RB binding protein 9, serine hydrolase
Plot
SH3 domain-binding glutamic acid-rich-like protein 2
Plot
aquaporin 3 (Gill blood group)
Plot
cationic trypsin-3
Plot
complement factor H-related protein 2-like
Plot
eukaryotic translation initiation factor 2B subunit epsilon
Plot
heat shock protein HSP 90-alpha-like
Plot
kelch domain containing 10
Plot
snRNA-activating protein complex subunit 5-like
Plot
trans-golgi network vesicle protein 23 homolog A
Plot
tripartite motif containing 21
Plot
ubiquinol-cytochrome-c reductase complex assembly factor 3
Plot
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Cluster 4 | Hits: 18

BPI fold containing family B member 3
Plot
NIMA related kinase 5
Plot
SEC14 like lipid binding 2
Plot
THAP domain containing 6
Plot
TNF receptor superfamily member 21
Plot
aldehyde dehydrogenase, dimeric NADP-preferring
Plot
ankyrin repeat domain-containing protein 26-like
Plot
anti-Mullerian hormone
Plot
armadillo repeat containing 3
Plot
capping actin protein of muscle Z-line subunit alpha 2
Plot
cytochrome c, testis-specific
Plot
family with sequence similarity 170 member A
Plot
glycosyltransferase 8 domain containing 2
Plot
guided entry of tail-anchored proteins factor 3, ATPase
Plot
histone H2B subacrosomal variant
Plot
karyopherin subunit alpha 7
Plot
serine/threonine kinase 40
Plot
transmembrane 7 superfamily member 2
Plot
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Cluster 5 | Hits: 17

A-kinase anchoring protein 8
Plot
N-terminal EF-hand calcium binding protein 2
Plot
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4-like
Plot
RNA binding protein, mRNA processing factor 2
Plot
actin filament associated protein 1 like 1
Plot
annexin A9
Plot
betaine--homocysteine S-methyltransferase
Plot
chaperonin containing TCP1 subunit 3
Plot
chromosome unknown C1orf232 homolog
Plot
crystallin lambda 1
Plot
lymphocyte transmembrane adaptor 1
Plot
mitochondrial nucleoid associated protein 1
Plot
programmed cell death 6 interacting protein
Plot
ribosomal protein S24
Plot
solute carrier family 43 member 3
Plot
transient receptor potential cation channel subfamily C member 1
Plot
triggering receptor expressed on myeloid cells 1
Plot
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Cluster 6 | Hits: 8

ALG11 alpha-1,2-mannosyltransferase
Plot
ATPase H+ transporting V0 subunit d1
Plot
ATPase H+ transporting V1 subunit C2
Plot
CKLF-like MARVEL transmembrane domain-containing protein 2
Plot
core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
Plot
phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 alpha
Plot
prolyl-tRNA synthetase associated domain-containing protein 1-like
Plot
zinc finger and BTB domain containing 38
Plot
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Stationary

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- Spline-type: Natural cubic spline
- DoF: 2
- Knots: NA
- Boundary-knots: NA -

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adj.p-value threshold: 0.050

Number of hits: 14

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Overall Clustering

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-Plot -
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-Plot -
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Min-max normalized individual and mean splines

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-Plot -
-
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-Plot -
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-Plot -
-
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Z-Score of log2 Value Heatmap

Rows = features (labels on the right, cluster labels on the left), columns = timepoints; Blue = down, red = up, --> compared to the rest - of the row;
-
-Plot -
-
-

Individual Significant Features (Hits) Splines

- Asterisks definition:
Adj. p-value < 0.05 --> *
Adj. p-value < 0.01 --> **
Adj. p-value < 0.001 --> ***
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Cluster 1 | Hits: 11

CD226 molecule
Plot
S100 calcium binding protein G
Plot
SEC61 translocon subunit alpha 2
Plot
SKI8 subunit of superkiller complex
Plot
adaptor related protein complex 5 subunit sigma 1
Plot
hemojuvelin BMP co-receptor
Plot
ribosomal protein S24
Plot
ribosomal protein S5
Plot
surfactant associated 2
Plot
trinucleotide repeat containing 18
Plot
ubiquitin like with PHD and ring finger domains 1
Plot
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Cluster 2 | Hits: 2

G2 and S-phase expressed 1
Plot
cadherin-6
Plot
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Cluster 3 | Hits: 1

COMM domain-containing protein 9
Plot
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