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 3130 to 3179 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1565 protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Subtracted 5602.01 6031.05 429.04
1566 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Divided 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
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Subtracted 6035.6 6464.5 428.9
1568 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Divided 5845.22 6267.34 1.07222
1569 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Subtracted 6035.6 6464.5 428.9
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Divided 5819.37 6239.55 1.0722
1570 mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Subtracted 6035.6 6464.5 428.9
n-acetylglutamate synthase. [refseq;acc:nm_153006] Divided 5162.27 5534.71 1.07215
1571 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] 5851.64 6273.4 1.07208
lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] Subtracted 6035.6 6464.5 428.9
1572 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] Divided 6068.03 6504.59 1.07194
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] Subtracted 6035.6 6464.5 428.9
1573 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Divided 11785.4 10995.3 1.07186
1574 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 5106.13 5472.96 1.07184
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Subtracted 6858.84 7287.27 428.43
1575 dc11 protein. [refseq;acc:nm_020186]
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Divided 5106.13 5472.96 1.07184
1576 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Subtracted 6858.84 7287.27 428.43
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] Divided 5923.66 6349.04 1.07181
1577 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524]
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Subtracted 6858.84 7287.27 428.43
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] Divided 6213.27 6659.39 1.0718
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Subtracted 6858.84 7287.27 428.43
1579 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Divided 5842.44 6261.87 1.07179
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Subtracted 4049 4477.43 428.43
1580 glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Divided 6376.12 6833.59 1.07175
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Subtracted 6858.84 7287.27 428.43
1581 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] Divided 6376.12 6833.59 1.07175
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] Subtracted 6858.84 7287.27 428.43
1582 melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194]
protein x 0001. [refseq;acc:nm_016302] Divided 6376.12 6833.59 1.07175
1583 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Subtracted 6858.84 7287.27 428.43
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Divided 6376.12 6833.59 1.07175
1584 calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Subtracted 6858.84 7287.27 428.43
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Divided 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
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Subtracted 6858.84 7287.27 428.43
1586 proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] 6112.4 6540.73 428.33
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] Divided 5784.36 6198.73 1.07164
1587 40s ribosomal protein s8. [swissprot;acc:p09058] Subtracted 5659.45 6087.55 428.1
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Divided 5784.36 6198.73 1.07164
1588 proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Subtracted 6180.24 6608.11 427.87
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 3600.99 3360.33 1.07162
1589 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Subtracted 5875.75 6302.76 427.01
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] Divided 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/