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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Network Comparison Type red Gene Rank Value Type description green Interaction Map Filtered network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 29840 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
red
Rank
description
green
network_comparison
212.74 2589 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 212.422 1.0015
212.793 2280 proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 211.657 1.00537
212.81 2283 proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 211.676 1.00536
212.816 2364 transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] 213.697 1.00414
212.833 1406 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 208.456 1.021
212.884 1829 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 215.323 1.01146
212.922 2730 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] 212.985 1.0003
2731 sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
212.945 1106 pxr2b protein. [refseq;acc:nm_016559] 207.109 1.02818
212.952 918 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 205.292 1.03731
212.953 2555 s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 212.572 1.00179
213.015 2273 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] 211.858 1.00546
213.021 2434 methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] 212.286 1.00346
213.048 2431 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] 212.3 1.00352
213.079 1228 glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] 218.325 1.02462
1229 glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506]
213.169 2646 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] 213.417 1.00116
2648 sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]
213.181 1579 cda11 protein. [refseq;acc:nm_032026] 209.732 1.01644
213.251 1489 mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] 209.264 1.01905
213.256 762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 203.237 1.0493
213.259 1518 [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] 209.524 1.01783
213.267 1515 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 209.511 1.01793
1516 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]
1517 seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]
213.268 1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 209.509 1.01794
1512 surfeit locus protein 1. [swissprot;acc:q15526]
1513 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]
1514 protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]
213.274 1507 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 209.5 1.01801
1508 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]
213.325 761 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 203.303 1.0493
213.347 2573 peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] 213.005 1.00161
213.351 1429 wd repeat domain 26. [refseq;acc:nm_025160] 217.74 1.02057
213.391 2259 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 214.606 1.00569
213.398 1500 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 209.52 1.01851
213.415 2583 dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] 213.743 1.00154
213.422 2576 beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 213.75
2578 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]
2579 nitrilase 1. [refseq;acc:nm_005600]
2580 utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
2582 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]
2584 dystrophin. [swissprot;acc:p11532]
2585 angiomotin. [refseq;acc:nm_133265]
2586 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
2587 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]
213.428 2581 dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] 213.756
213.494 2545 proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 213.088 1.00191
213.546 1542 trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] 209.965 1.01706
1543 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]

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/