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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6258 to 6307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1565 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Squared 29530.9 32827.2 1.11162
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Measured 6343.76 6803.44 1.07246
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Rooted 64.5103 66.8259 1.0359
1566 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Ranked 221.128 224.767 1.01646
eyes absent homolog 1. [swissprot;acc:q99502] Rooted 61.9761 64.2003 1.03589
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Squared 2565.98 2308.67 1.11145
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Measured 5846.67 6269.41 1.0723
1567 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 5822.25 6242.94 1.07226
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Ranked 221.128 224.767 1.01646
megf11 protein. [refseq;acc:nm_032445] Squared 29503.9 32791.7 1.11144
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Rooted 61.97 64.1935 1.03588
1568 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Ranked 221.128 224.767 1.01646
megf10 protein. [refseq;acc:nm_032446] Squared 29503.5 32791.2 1.11143
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Measured 5845.22 6267.34 1.07222
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Rooted 61.9702 64.1936 1.03588
1569 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 61.9705 64.1938
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Squared 29502.7 32790.1 1.11143
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Ranked 221.128 224.767 1.01646
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Measured 5819.37 6239.55 1.0722
1570 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Squared 26688.8 29658.6 1.11128
n-acetylglutamate synthase. [refseq;acc:nm_153006] Measured 5162.27 5534.71 1.07215
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked 221.128 224.767 1.01646
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Rooted 61.9703 64.1936 1.03588
1571 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Measured 5851.64 6273.4 1.07208
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Ranked 221.128 224.767 1.01646
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Squared 22613.3 25129.4 1.11127
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Rooted 61.9703 64.1936 1.03588
1572 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Squared 22613.3 25129.4 1.11127
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Rooted 61.9703 64.1936 1.03588
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Measured 6068.03 6504.59 1.07194
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Ranked 221.128 224.767 1.01646
1573 adaptor-associated kinase 1. [refseq;acc:nm_014911] Rooted 61.9703 64.1936 1.03588
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Measured 11785.4 10995.3 1.07186
r3h domain protein 1. [swissprot;acc:q15032] Ranked 218.105 214.573 1.01646
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Squared 17375.5 19308.1 1.11123
1574 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 29470.8 32748.2 1.11121
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Measured 5106.13 5472.96 1.07184
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Rooted 61.9701 64.1935 1.03588
tata element modulatory factor (tmf). [swissprot;acc:p82094] Ranked 222.585 218.982 1.01645
1575 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Rooted 61.9703 64.1936 1.03588
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Measured 5106.13 5472.96 1.07184
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Squared 28606.1 31783.4 1.11107
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Ranked 222.585 218.982 1.01645
1576 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Squared 28606.1 31783.4 1.11107
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] Measured 5923.66 6349.04 1.07181
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Ranked 222.585 218.982 1.01645
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Rooted 61.9703 64.1936 1.03588
1577 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] Measured 5923.66 6349.04 1.07181
ammecr1 protein. [refseq;acc:nm_015365] Ranked 222.585 218.982 1.01645
protein x 0001. [refseq;acc:nm_016302] Squared 28606.1 31783.4 1.11107

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/