Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2777 to 2826 of 3228 in total

Value Type: Ranked
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1
red: 0.00001
green: 0.00001
network\_comparison: 1

\def\wcA{0.33333333333333\textwidth}
\def\wcB{0.33333333333333\textwidth}
\begin{longtable}{|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2777\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2778\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2779\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2780\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2781\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
exocyst complex component exo70. [source:swissprot;acc:q9upt5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2782\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [source:swissprot;acc:o75787]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2783\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mab-21-like protein 2; mab-21-like 2. [source:refseq;acc:nm\_006439]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2784\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a.a (h2a/a) (h2a.2). [source:swissprot;acc:p28001]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2785\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [source:swissprot;acc:p06748]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2786\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mab-21-like protein 1; mab-21-like 1. [source:refseq;acc:nm\_005584]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2787\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
high mobility group protein 4-like (hmg-4l). [source:swissprot;acc:q9uj13]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2788\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [source:swissprot;acc:p24588]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2789\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [source:swissprot;acc:q06124]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2790\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [source:swissprot;acc:q9y5q3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2791\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [source:swissprot;acc:p20674]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2792\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor maf (proto-oncogene c-maf). [source:swissprot;acc:o75444]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2793\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [source:swissprot;acc:o75795]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2794\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm\_015503]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2795\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [source:swissprot;acc:p19404]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2796\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [source:swissprot;acc:q9npf5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2797\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sperm tail protein shippo1; h-shippo 1. [source:refseq;acc:nm\_053280]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2798\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2799\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hmg2 like. [source:refseq;acc:nm\_145205]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2800\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mondoa. [source:refseq;acc:nm\_014938]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2801\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [source:swissprot;acc:q92889]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2802\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [source:swissprot;acc:p14060]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2803\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nanos (fragment). [source:sptrembl;acc:q8wy41]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2804\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
barrier-to-autointegration factor (breakpoint cluster region protein 1). [source:swissprot;acc:o75531]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2805\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [source:refseq;acc:nm\_018026]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2806\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
spry domain-containing socs box protein ssb-4. [source:refseq;acc:nm\_080862]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2807\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-related protein rab-1b. [source:swissprot;acc:q9h0u4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2808\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [source:swissprot;acc:p49917]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2809\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [source:refseq;acc:nm\_024947]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2810\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [source:refseq;acc:nm\_006798]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2811\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [source:swissprot;acc:p49765]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2812\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mob-lak. [source:refseq;acc:nm\_130807]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2813\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone deacetylase 3 (hd3) (rpd3-2). [source:swissprot;acc:o15379]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2814\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
spry domain-containing socs box protein ssb-1. [source:refseq;acc:nm\_025106]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2815\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
g protein-coupled receptor 66. [source:refseq;acc:nm\_006056]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2816\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tigger transposable element derived 1; jerky (mouse) homolog-like. [source:refseq;acc:nm\_145702]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2817\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [source:swissprot;acc:o75347]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2818\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [source:swissprot;acc:p16662]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2819\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:o75310]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2820\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [source:swissprot;acc:p55201]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2821\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vacuolar proton-atpase subunit. [source:sptrembl;acc:q8nhe4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2822\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
zinc transporter 1 (znt-1). [source:swissprot;acc:q9y6m5]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2823\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nuclear factor related to kappa b binding protein. [source:refseq;acc:nm\_006165]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2824\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [source:swissprot;acc:q16082]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2825\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2826\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
suppressor of actin 1. [source:refseq;acc:nm\_014016]\vspace{3pt}}\\\hline
nd{longtable}

Legend:
- Rank is the rank after comparing the two networks

 - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray

 - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.

 - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them

 - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.

 - Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/