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.


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Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 25 to 74 of 473 in total 
Network Comparison Type: Subtracted
Value Type: Ranked
Interaction Map: High confidence
Filtered: 1
red: 0
green: 0
network\_comparison: 0

\def\wcA{0.25\textwidth}
\def\wcB{0.25\textwidth}
\def\wcC{0.25\textwidth}
\begin{longtable}{|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Hugo\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
description\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2780\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
KPNA2\vspace{3pt}}&\parbox{\wcC}{\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
EXOC7\vspace{3pt}}&\parbox{\wcC}{\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
ATP6AP2\vspace{3pt}}&\parbox{\wcC}{\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
MAB21L2\vspace{3pt}}&\parbox{\wcC}{\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
HIST3H2A\vspace{3pt}}&\parbox{\wcC}{\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
NPM1\vspace{3pt}}&\parbox{\wcC}{\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
MAB21L1\vspace{3pt}}&\parbox{\wcC}{\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
HMG4L\vspace{3pt}}&\parbox{\wcC}{\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
AKAP5\vspace{3pt}}&\parbox{\wcC}{\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
PTPN11\vspace{3pt}}&\parbox{\wcC}{\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
\vspace{3pt}}&\parbox{\wcC}{\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
COX5A\vspace{3pt}}&\parbox{\wcC}{\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
MAF\vspace{3pt}}&\parbox{\wcC}{\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
\vspace{3pt}}&\parbox{\wcC}{\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
SH2B1\vspace{3pt}}&\parbox{\wcC}{\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
NDUFV2\vspace{3pt}}&\parbox{\wcC}{\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
DMAP1\vspace{3pt}}&\parbox{\wcC}{\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
ODF3\vspace{3pt}}&\parbox{\wcC}{\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
ARIH2\vspace{3pt}}&\parbox{\wcC}{\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
HMGB4\vspace{3pt}}&\parbox{\wcC}{\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
MLXIP\vspace{3pt}}&\parbox{\wcC}{\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
ERCC4\vspace{3pt}}&\parbox{\wcC}{\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}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\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}}\\\cline{1-1}\cline{3-3}
\parbox{\wcA}{\vspace{3pt}\noindent
2803\vspace{3pt}}&&\parbox{\wcC}{\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
BANF1\vspace{3pt}}&\parbox{\wcC}{\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
PACS1\vspace{3pt}}&\parbox{\wcC}{\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
SPSB4\vspace{3pt}}&\parbox{\wcC}{\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
RAB1C\vspace{3pt}}&\parbox{\wcC}{\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
LIG4\vspace{3pt}}&\parbox{\wcC}{\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
PHC3\vspace{3pt}}&\parbox{\wcC}{\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
UGT2A1\vspace{3pt}}&\parbox{\wcC}{\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
VEGFB\vspace{3pt}}&\parbox{\wcC}{\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
MOBKL2A\vspace{3pt}}&\parbox{\wcC}{\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
HDAC3\vspace{3pt}}&\parbox{\wcC}{\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
SPSB1\vspace{3pt}}&\parbox{\wcC}{\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
NMUR1\vspace{3pt}}&\parbox{\wcC}{\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
TIGD1\vspace{3pt}}&\parbox{\wcC}{\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
TBCA\vspace{3pt}}&\parbox{\wcC}{\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
UGT2B7\vspace{3pt}}&\parbox{\wcC}{\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}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:o75310]\vspace{3pt}}\\\cline{1-1}\cline{3-3}
\parbox{\wcA}{\vspace{3pt}\noindent
2820\vspace{3pt}}&&\parbox{\wcC}{\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
ATP6V0E2\vspace{3pt}}&\parbox{\wcC}{\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
SLC30A1\vspace{3pt}}&\parbox{\wcC}{\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
NFRKB\vspace{3pt}}&\parbox{\wcC}{\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
HSPB2\vspace{3pt}}&\parbox{\wcC}{\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}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
mitochondrial 28s ribosomal protein s6 (mrp-s6). [source:swissprot;acc:p82932]\vspace{3pt}}\\\cline{1-1}\cline{3-3}
\parbox{\wcA}{\vspace{3pt}\noindent
2826\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
suppressor of actin 1. [source:refseq;acc:nm\_014016]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2827\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
GPS1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [source:swissprot;acc:q13098]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2828\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [source:swissprot;acc:p51966]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2829\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ASPSCR1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm\_024083]\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

 - Hugo is the HGNC identifier if it exists

 - 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/