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 Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 3228 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 2360 3843.06 3682.72 1.04354
60s ribosomal protein l5. [swissprot;acc:p46777] 2169 3639.65 3459.64 1.05203
60s ribosomal protein l7. [swissprot;acc:p18124] 2308 3976.92 3804.85 1.04522
60s ribosomal protein l8. [swissprot;acc:p25120] 386 4533.74 5279.4 1.16447
60s ribosomal protein l9. [swissprot;acc:p32969] 2225 3750.99 3580.35 1.04766
65 kda yes-associated protein (yap65). [swissprot;acc:p46937] 1459 5672.25 6104.01 1.07612
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084] 3227 0.00001 0.00001 1
9 kda protein. [swissprot;acc:p13994] 1461 5672.25 6104.01 1.07612
a kindred of iglon. [refseq;acc:nm_173808] 2712 5603.24 5583.64 1.00351
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] 2788 0.00001 0.00001 1
a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 192 17757.5 14008 1.26767
aarf domain containing kinase 1. [refseq;acc:nm_020421] 1177 5799.35 6305.95 1.08735
aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] 1175
aarf domain containing kinase 4. [refseq;acc:nm_024876] 1176
abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 2223 5864.49 6145.14 1.04786
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 1333 5803.95 6269.44 1.0802
acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] 2304 6946.38 7263.48 1.04565
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 1514 7232.14 7768.35 1.07414
acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 1509 7237.39 7775.21 1.07431
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 2342 7007.72 7317.15 1.04416
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 1893 6830.4 7261.98 1.06319
acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 1172 5826.32 6335.95 1.08747
actin binding lim protein 2. [refseq;acc:nm_032432] 1012 5791.82 6340.86 1.0948
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 1354 6036.22 6512.64 1.07893
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 1020 5791.82 6340.86 1.0948
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] 1778 5386.37 5744.89 1.06656
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] 1783
actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] 1786
activated p21cdc42hs kinase. [refseq;acc:nm_005781] 1055 4757.46 5198.91 1.09279
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 1146 6281.21 6837.61 1.08858
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 2435 3669.33 3797.78 1.03501
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 2160 5379.55 5660.25 1.05218
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771] 3050 0.00001 0.00001 1
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] 1917 6858.84 7287.27 1.06246
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] 2612 6380.61 6476.19 1.01498
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 1620 6296.52 6743.85 1.07104
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 380 12998.5 15138.2 1.16461
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] 2035 6920.71 7315.59 1.05706
acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 2154 6884.69 7247.36 1.05268
ad24 protein. [refseq;acc:nm_022451] 445 3753.71 4315.95 1.14978
adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] 1530 5916.05 6350.53 1.07344
adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 2064 5548.79 5861.31 1.05632
adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] 2059 5552.69 5865.84 1.0564
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 2062 5552.7 5865.85
adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] 2061 5552.69 5865.84
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 2058
adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] 2060
adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] 2050 5556.36 5870.11 1.05647
adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 2623 6815.24 6916.14 1.01481
adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] 2625

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/