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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 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
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
\parbox{\wcA}{\vspace{3pt}\noindent
2827\vspace{3pt}}&\parbox{\wcB}{\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
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
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
\parbox{\wcA}{\vspace{3pt}\noindent
2830\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [source:swissprot;acc:q9hcp0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2831\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [source:swissprot;acc:p39748]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2832\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
semaphorin 6b precursor (semaphorin z) (sema z). [source:swissprot;acc:q9h3t3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2833\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [source:swissprot;acc:p07226]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2834\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2835\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [source:swissprot;acc:p19224]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2836\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
conserved oligomeric golgi complex component 1. [source:swissprot;acc:q8wtw3]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2837\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [source:swissprot;acc:o00142]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2838\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [source:swissprot;acc:q96jq0]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2839\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [source:swissprot;acc:q12962]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2840\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [source:swissprot;acc:q93034]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2841\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cop9 signalosome complex subunit 2 (signalosome subunit 2) (sgn2) (thyroid receptor interacting protein 15) (trip15). [source:swissprot;acc:q15647]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2842\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [source:swissprot;acc:q14978]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2843\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [source:swissprot;acc:q96ld8]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2844\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
fibrillin 1 precursor. [source:swissprot;acc:p35555]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2845\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [source:swissprot;acc:q9uks6]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2846\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ctcl tumor antigen l14-2. [source:refseq;acc:nm\_018017]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2847\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dachshund homolog isoform a. [source:refseq;acc:nm\_080759]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2848\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [source:swissprot;acc:p52655]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2849\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [source:swissprot;acc:q92966]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2850\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [source:swissprot;acc:q00535]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2851\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
origin recognition complex subunit 5. [source:swissprot;acc:o43913]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2852\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
histone h2a; h2a histone family, member r. [source:refseq;acc:nm\_170745]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2853\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
tigger transposable element derived 6. [source:refseq;acc:nm\_030953]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2854\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [source:refseq;acc:nm\_057175]\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
2855\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]\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/