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 3132 to 3181 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1566 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] High confidence 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
voltage-dependent anion-selective channel protein 3 (vdac-3) (hvdac3) (outer mitochondrial membrane protein porin 3). [swissprot;acc:q9y277] Low confidence 8243.89 8522.47 1.03379
1568 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] High confidence 5845.22 6267.34 1.07222
voltage-dependent anion-selective channel protein 1 (vdac-1) (hvdac1) (outer mitochondrial membrane protein porin 1) (plasmalemmal porin) (porin 31hl) (porin 31hm). [swissprot;acc:p21796] Low confidence 8243.37 8521.94 1.03379
1569 traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] High confidence 5819.37 6239.55 1.0722
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Low confidence 7085.19 7324.62 1.03379
1570 n-acetylglutamate synthase. [refseq;acc:nm_153006] High confidence 5162.27 5534.71 1.07215
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476] Low confidence 8056.49 8328.64 1.03378
1571 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] High confidence 5851.64 6273.4 1.07208
isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] Low confidence 8100.76 8374.39 1.03378
1572 metastasis-associated protein mta1. [swissprot;acc:q13330] 7697.8 7957.79 1.03377
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] High confidence 6068.03 6504.59 1.07194
1573 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] 11785.4 10995.3 1.07186
voltage-dependent anion-selective channel protein 2 (vdac-2) (hvdac2) (outer mitochondrial membrane protein porin 2). [swissprot;acc:p45880] Low confidence 8242.31 8520.63 1.03377
1574 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] High confidence 5106.13 5472.96 1.07184
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Low confidence 7846.35 8111.3 1.03377
1575 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] High confidence 5106.13 5472.96 1.07184
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Low confidence 8004.96 8275.26 1.03377
1576 mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] High confidence 5923.66 6349.04 1.07181
ras-related protein rab-1b. [swissprot;acc:q9h0u4] Low confidence 8057.74 8329.74 1.03376
1577 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] High confidence 5923.66 6349.04 1.07181
tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063] Low confidence 7797.17 8060.42 1.03376
1578 proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] High confidence 6213.27 6659.39 1.0718
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Low confidence 7999.79 8269.83 1.03376
1579 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] High confidence 5842.44 6261.87 1.07179
atp-binding cassette, sub-family f, member 2 (iron inhibited abc transporter 2) (hussy-18). [swissprot;acc:q9ug63] Low confidence 7973.8 8243.03 1.03376
1580 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] High confidence 6376.12 6833.59 1.07175
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 4, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 4). [swissprot;acc:q16654] Low confidence 7797.23 8060.47 1.03376
1581 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] High confidence 6376.12 6833.59 1.07175
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 3, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 3). [swissprot;acc:q15120] Low confidence 7797.52 8060.71 1.03375
1582 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 8125.54 8399.69 1.03374
protein x 0001. [refseq;acc:nm_016302] High confidence 6376.12 6833.59 1.07175
1583 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Low confidence 8074.15 8346.55 1.03374
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] High confidence 6376.12 6833.59 1.07175
1584 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Low confidence 8213.09 8490.12 1.03373
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] High confidence 5933.25 6358.78 1.07172
1585 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] 5858.48 6278.32 1.07166
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Low confidence 7638.21 7895.81 1.03373
1586 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 8019.5 8289.89 1.03372
ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] High confidence 5784.36 6198.73 1.07164
1587 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Low confidence 7807.26 8070.46 1.03371
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] High confidence 5784.36 6198.73 1.07164
1588 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Low confidence 8146.85 8421.4 1.0337
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] High confidence 3600.99 3360.33 1.07162
1589 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
serine/threonine kinase 38; serine threonine protein kinase. [refseq;acc:nm_007271] Low confidence 8152.72 8427.49 1.0337
1590 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] High confidence 6364.01 6819.38 1.07155
ras-related protein rab-5b. [swissprot;acc:p35239] Low confidence 7969.92 8238.53 1.0337
1591 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] High confidence 6364.01 6819.38 1.07155

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/