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 green Interaction Map Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
green
Interaction Map
red
network_comparison
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 4467 210.017 Low confidence 208.138 1.00903
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 1608 195.607 199.691 1.02088
2067 191.639 High confidence 193.226 1.00828
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 1192 194.529 Low confidence 199.02 1.02309
1661 201.551 High confidence 204.437 1.01432
adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 1200 194.493 Low confidence 198.973 1.02303
1665 201.564 High confidence 204.433 1.01423
adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 1701 197.403 Low confidence 201.46 1.02055
1850 213.587 High confidence 215.931 1.01097
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 1699 197.367 Low confidence 201.425 1.02056
1895 213.639 High confidence 215.853 1.01036
adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] 2369 219.434 218.555 1.00402
2525 199.602 Low confidence 203.221 1.01813
adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] 813 221.785 High confidence 212.386 1.04425
3843 198.793 Low confidence 201.394 1.01308
adiponectin receptor 2. [refseq;acc:nm_024551] 104 204.212 219.277 1.07377
185 246.371 High confidence 281.582 1.14292
adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] 1552 221.424 225.159 1.01687
1779 195.272 Low confidence 199.221 1.02022
adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] 1551 221.424 High confidence 225.159 1.01687
1772 195.276 Low confidence 199.226 1.02023
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 1550 221.424 High confidence 225.159 1.01687
1780 195.256 Low confidence 199.201 1.0202
adp-ribose pyrophosphatase (ec 3.6.1.13) (adp-ribose diphosphatase) (adenosine diphosphoribose pyrophosphatase) (adpr-ppase) (adp-ribose phosphohydrolase) (nucleoside diphosphate-linked moiety x motif 9). [swissprot;acc:q9bw91] 2492 200.307 203.957 1.01822
adp-ribosylation factor 1. [swissprot;acc:p32889] 1229 198.315 202.83 1.02277
2128 222.788 High confidence 221.248 1.00696
adp-ribosylation factor 3. [swissprot;acc:p16587] 1164 198.252 Low confidence 202.869 1.02329
2130 222.788 High confidence 221.248 1.00696
adp-ribosylation factor 4. [swissprot;acc:p18085] 1165 198.216 Low confidence 202.831 1.02328
2123 222.788 High confidence 221.248 1.00696
adp-ribosylation factor 5. [swissprot;acc:p26437] 3558 196.554 Low confidence 199.425 1.01461
adp-ribosylation factor binding protein gga1 (golgi-localized, gamma ear-containing, arf-binding protein 1) (gamma-adaptin related protein 1). [swissprot;acc:q9ujy5] 3022 196.696 199.98 1.0167
adp-ribosylation factor binding protein gga2 (golgi-localized, gamma ear-containing, arf-binding protein 2) (gamma-adaptin related protein 2) (vear) (vhs domain and ear domain of gamma-adaptin). [swissprot;acc:q9ujy4] 3016 196.697 199.984 1.01671
adp-ribosylation factor binding protein gga3 (golgi-localized, gamma ear-containing, arf-binding protein 3). [swissprot;acc:q9nz52] 3030 196.693 199.971 1.01667
adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] 2156 198.71 High confidence 200.063 1.00681
2704 195.675 Low confidence 199.109 1.01755
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 2137 222.788 High confidence 221.248 1.00696
3196 197.655 Low confidence 200.829 1.01606
adp-ribosylation factor guanine nucleotide factor 6; hepatocellular carcinoma-associated antigen 67. [refseq;acc:nm_015310] 4149 198.625 200.724 1.01057
adp-ribosylation factor-like protein 1. [swissprot;acc:p40616] 2613 215.799 High confidence 215.497 1.0014
4075 198.695 Low confidence 200.896 1.01108
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] 2520 216.341 High confidence 215.835 1.00234
4553 200.827 Low confidence 202.436 1.00801
adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] 1188 212.904 High confidence 218.402 1.02582
2587 194.454 Low confidence 197.95 1.01798
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 212.904 High confidence 218.402 1.02582
2585 194.454 Low confidence 197.95 1.01798
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 1074 187.103 191.57 1.02387
1105 185.882 High confidence 191.139 1.02828
adrenoleukodystrophy protein (aldp). [swissprot;acc:p33897] 1553 206.704 Low confidence 202.418 1.02117

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/