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 801 to 850 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 5201.41 4479.76 1.16109
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Low confidence 10800.7 10260 1.0527
402 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 5201.41 4479.76 1.16109
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 7934.21 8352.26 1.05269
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] High confidence 5201.41 4479.76 1.16109
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Low confidence 8853.13 9319.56 1.05269
404 kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] 10008.8 9508.16 1.05265
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 5201.41 4479.76 1.16109
405 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Low confidence 10008.8 9508.16 1.05265
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 5201.41 4479.76 1.16109
406 l-lactate dehydrogenase a-like (ec 1.1.1.27). [swissprot;acc:q9byz2] Low confidence 6973.3 7340.34 1.05264
thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 5201.41 4479.76 1.16109
407 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Low confidence 6634.26 6983.5 1.05264
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] High confidence 6603.41 7664.65 1.16071
408 dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 1.1604
l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] Low confidence 6973.31 7340.35 1.05263
409 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] High confidence 6102.59 7081.46 1.1604
l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] Low confidence 6973.32 7340.36 1.05263
410 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] High confidence 6102.59 7081.46 1.1604
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Low confidence 6973.61 7340.61 1.05263
411 l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195] 6973.35 7340.39
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] High confidence 6102.59 7081.46 1.1604
412 clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] Low confidence 6973.35 7340.39 1.05263
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 3594.31 4169.95 1.16015
413 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence 6974.82 7341.65 1.05259
vav proto-oncogene. [swissprot;acc:p15498] High confidence 6644.99 7707.8 1.15994
414 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 6744.05 5815.13 1.15974
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Low confidence 6975.39 7342.13 1.05258
415 hn1 like. [refseq;acc:nm_144570] 8657.07 9111.9 1.05254
vav-3 protein. [swissprot;acc:q9ukw4] High confidence 6647.43 7706.18 1.15927
416 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 4509.54 5223.95 1.15842
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] Low confidence 6972.28 7338.33 1.0525
417 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] 7902.1 8316.41 1.05243
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] High confidence 4522.71 5233.14 1.15708
418 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 5493.1 6350.19 1.15603
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Low confidence 8958.02 9427.3 1.05239
419 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 8768.68 9227.9 1.05237
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] High confidence 5493.1 6350.19 1.15603
420 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 10235.2 11830.8 1.15589
latrophilin 3; latrophilin homolog 3 (cow); lectomedin 3. [refseq;acc:nm_015236] Low confidence 8768.68 9227.9 1.05237
421 latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302]
vav-2 protein. [swissprot;acc:p52735] High confidence 6660.02 7697.78 1.15582
422 latrophilin 1; lectomedin-2; latrophilin homolog 1 (cow). [refseq;acc:nm_014921] Low confidence 8768.68 9227.9 1.05237
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] High confidence 5206.9 6010.04 1.15425
423 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 5207.03 6010.1 1.15423
protein tyrosine phosphatase, non-receptor type 14 (ec 3.1.3.48) (protein-tyrosine phosphatase pez). [swissprot;acc:q15678] Low confidence 8902.76 9368.39 1.0523
424 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] High confidence 5207.78 6010.45 1.15413
protein tyrosine phosphatase, non-receptor type 21 (ec 3.1.3.48) (protein-tyrosine phosphatase d1). [swissprot;acc:q16825] Low confidence 8902.76 9368.39 1.0523
425 ras-related protein rab-7. [swissprot;acc:p51149] 8055.75 8476.72 1.05226
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 3729.02 4301.58 1.15354

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/