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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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 network_comparison green
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
network_comparison
green
1853 tubulin-tyrosine ligase. [refseq;acc:nm_153712] Ranked 217.924 1.01095 215.564
1854 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Rooted 62.7784 1.02965 64.64
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Measured 6076.66 1.0636 6463.14
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Ranked 222.215 1.0109 224.637
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Squared 26167.1 1.09581 28674.2
1855 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Rooted 62.7784 1.02965 64.64
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Ranked 217.891 1.0109 215.542
keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Measured 6076.66 1.0636 6463.14
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Squared 26167.1 1.09581 28674.2
1856 dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Rooted 62.7784 1.02965 64.64
dystrophin. [swissprot;acc:p11532] Squared 26167.1 1.09581 28674.2
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Ranked 217.892 1.0109 215.543
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Measured 6076.66 1.0636 6463.14
1857 angiomotin. [refseq;acc:nm_133265] Squared 26167.1 1.09581 28674.2
ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Rooted 62.7784 1.02965 64.64
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Measured 6076.66 1.0636 6463.15
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Ranked 222.215 1.0109 224.637
1858 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] Squared 26167.1 1.09581 28674.2
ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Rooted 62.7784 1.02965 64.64
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Ranked 217.893 1.01089 215.545
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Measured 6076.66 1.0636 6463.13
1859 adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Rooted 62.7784 1.02965 64.64
alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] Squared 26167.1 1.09581 28674.2
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Ranked 217.895 1.01089 215.547
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Measured 6076.66 1.0636 6463.13
1860 dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] Squared 26167.2 1.0958 28674.1
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Ranked 217.895 1.01089 215.547
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 6076.66 1.0636 6463.13
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Rooted 62.7784 1.02965 64.64
1861 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
beta-catenin (pro2286). [swissprot;acc:p35222] Squared 26746.2 1.09561 29303.5
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Ranked 210.856 1.01087 213.147
keratin associated protein 1.5. [refseq;acc:nm_031957] Measured 6076.66 1.0636 6463.14
1862 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Ranked 210.856 1.01087 213.147
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Squared 14336.6 1.09553 15706.2
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Rooted 63.2302 1.0296 65.1018
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured 6076.66 1.0636 6463.13
1863 g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Squared 26779 1.09552 29336.9
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Measured 6076.66 1.0636 6463.14
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Ranked 210.856 1.01087 213.147
nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946] Rooted 63.2302 1.0296 65.1018
1864 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Ranked 203.071 1.01086 200.89
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Squared 26778.4 1.09552 29336.2
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured 6076.66 1.0636 6463.14
lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Rooted 63.2302 1.0296 65.1018
1865 eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Ranked 221.639 1.01086 224.046
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Squared 26777.3 1.09551 29334.8
mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Rooted 63.2302 1.0296 65.1018
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Measured 6076.66 1.0636 6463.12
1866 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Squared 26776.3 1.09551 29333.6

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/