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 1230 to 1279 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
615 frataxin, mitochondrial precursor (friedreich's ataxia protein) (fxn). [swissprot;acc:q16595] Low confidence 8653.9 9043.68 1.04504
616 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] High confidence 11222.2 9948.93 1.12798
xaa-pro aminopeptidase 2 precursor (ec 3.4.11.9) (x-pro aminopeptidase 2) (membrane-bound aminopeptidase p) (membrane-bound app) (membrane- bound amp) (mamp) (aminoacylproline aminopeptidase). [swissprot;acc:o43895] Low confidence 8653.9 9043.68 1.04504
617 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] High confidence 5162.52 5822.47 1.12783
mitochondrial glutamate carrier 1. [refseq;acc:nm_024698] Low confidence 8906.67 9307.73 1.04503
618 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] High confidence 7878.27 8879.08 1.12703
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Low confidence 7790.89 8141.64 1.04502
619 nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] High confidence 3879.99 4371.24 1.12661
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Low confidence 7790.91 8141.69 1.04502
620 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] High confidence 6227.87 7012.9 1.12605
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 7142.69 7464.2 1.04501
621 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] High confidence 4115.39 4633.96 1.12601
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence 7147.13 7468.76 1.045
622 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] High confidence 6228.42 7013.21 1.126
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 7147.25 7468.88 1.045
623 calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] 8450.51 8830.8
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] High confidence 6228.39 7013.19 1.126
624 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Low confidence 7147.24 7468.87 1.045
625 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] High confidence 6228.39 7013.19 1.126
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 7147.24 7468.87 1.045
626 myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 7147.13 7468.76
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] High confidence 6228.39 7013.19 1.126
627 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Low confidence 7150.57 7472.28 1.04499
limkain b1. [refseq;acc:nm_019081] High confidence 6228.39 7013.19 1.126
628 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Low confidence 7436.09 7770.06 1.04491
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] High confidence 6228.39 7013.19 1.126
629 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]
g10 protein homolog (edg-2). [swissprot;acc:p41223] Low confidence 7932.4 8288.53 1.0449
630 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] High confidence 6228.39 7013.19 1.126
glutamyl trna synthetase. [sptrembl;acc:o14563] Low confidence 8348.4 8723.11 1.04488
631 17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 8316.12 8689.28 1.04487
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] High confidence 6228.39 7013.19 1.126
632 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
estradiol 17 beta-dehydrogenase 7 (ec 1.1.1.62) (17-beta-hsd 7) (17- beta-hydroxysteroid dehydrogenase 7). [swissprot;acc:p56937] Low confidence 8315.33 8688.21 1.04484
633 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] High confidence 6228.39 7013.19 1.126
tpa regulated locus; uncharacterized hypothalamus protein htmp. [refseq;acc:nm_018475] Low confidence 8331.28 8704.52 1.0448
634 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 7262.59 7587.85 1.04479
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] High confidence 6228.39 7013.19 1.126
635 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Low confidence 7262.13 7587.39 1.04479
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] High confidence 6228.97 7013.53 1.12595
636 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Low confidence 7262.73 7587.97 1.04478
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] High confidence 5713.41 6432.92 1.12593
637 putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] 7756.51 8731.76 1.12573
ubiquitin-conjugating enzyme e2 m (ec 6.3.2.19) (ubiquitin-protein ligase m) (ubiquitin carrier protein m) (nedd8-conjugating enzyme ubc12). [swissprot;acc:o76069] Low confidence 8025.21 8384.21 1.04473
638 nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] High confidence 7755.69 8730.74 1.12572
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Low confidence 7720 8065.07 1.0447
639 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 7686.11 8029.54 1.04468
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] High confidence 7753.59 8728.13 1.12569
640 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 4811.02 5414.64 1.12547

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/