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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 473 in total

Value Type: Measured
Interaction Map: High confidence
Network Comparison Type: Subtracted
Filtered: 1
red: 0
green: 0
network\_comparison: 0

\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
2756\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2757\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2758\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2759\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2760\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2761\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2762\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2763\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ring finger protein 3. [source:refseq;acc:nm\_006315]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2764\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2765\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a.e (h2a/e). [source:swissprot;acc:q99878]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2766\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2767\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2768\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a.x (h2a/x). [source:swissprot;acc:p16104]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2769\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2770\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nipsnap1 protein. [source:swissprot;acc:q9bpw8]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2771\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2772\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm\_177533]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2773\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2774\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dc12 protein. [source:refseq;acc:nm\_020187]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2775\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2776\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm\_017745]\vspace{3pt}}\\\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
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/