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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description Gene Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 568 to 617 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
Interaction Map
Filtered
red
green
network_comparison
adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 3896 Low confidence 1 8131.89 8321.51 1.02332
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979] 2870 High confidence 0.00001 0.00001 1
3865 Low confidence 8199.38 8392.72 1.02358
adaptor-associated kinase 1. [refseq;acc:nm_014911] 2219 8104.37 8358.61 1.03137
2282 High confidence 5783.73 6048.91 1.04585
adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] 1067 Low confidence 7794.59 8086.72 1.03748
2007 High confidence 5684.61 6018.72 1.05877
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 295 0 426.8 384.843 1.10902
626 Low confidence 5201.75 5361.78 1.03076
1063 1 7793.78 8086.18 1.03752
2010 High confidence 5671.62 6003.67 1.05855
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 374 0 2323.8 2452.23 1.05527
579 Low confidence 1842.51 1922.24 1.04327
2104 1 8183.03 8442.79 1.03174
2519 High confidence 5964.17 6113.96 1.02511
adenomatous polyposis coli like. [refseq;acc:nm_005883] 174 Low confidence 0 2544.19 3114.19 1.22404
4706 1 6234.4 6148.55 1.01396
adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] 4710 6233.66 6148.69 1.01382
adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] 146 0 1073.89 835.57 1.28522
1358 1 8000.32 8280.09 1.03497
adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263] 1581 High confidence 6376.12 6833.59 1.07175
2072 Low confidence 8133.86 8392.72 1.03182
adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 940 High confidence 5568.96 6113.35 1.09775
3058 Low confidence 8048.72 8272.77 1.02784
adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] 1851 High confidence 6156.28 6549.03 1.0638
2776 Low confidence 8010.75 8244.63 1.0292
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 401 High confidence 5201.41 4479.76 1.16109
3159 Low confidence 7975.92 8194.54 1.02741
adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 400 High confidence 5201.41 4479.76 1.16109
3158 Low confidence 7975.92 8194.54 1.02741
adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 2385 High confidence 3716.43 3569.68 1.04111
4422 Low confidence 8168.38 8329 1.01966
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 347 High confidence 0 1491.75 1591.6 1.06693
484 Low confidence 1344.45 1431.5 1.06475
2228 High confidence 1 3650.82 3484.97 1.04759
4696 Low confidence 7409.04 7516.41 1.01449
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 1640 High confidence 7444.28 7964 1.06981
1704 Low confidence 8171.93 8443.14 1.03319
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 479 High confidence 0 1318.37 1310.67 1.00587
505 Low confidence 2027.06 1913.73 1.05922
548 1 8447.46 8841.77 1.04668
679 High confidence 6503.1 7282.94 1.11992
adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 546 Low confidence 8451.27 8845.91 1.0467
680 High confidence 6503.03 7282.5 1.11986
adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 1541 5989.3 6427.17 1.07311
2524 Low confidence 8100.8 8345.7 1.03023
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 262 High confidence 0 764.479 676.971 1.12926
707 Low confidence 2355.39 2316.06 1.01698
1562 High confidence 1 5984.88 6419.11 1.07255
2537 Low confidence 8104.44 8349.23 1.0302

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/