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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Filtered Gene Value Type description Rank Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 101 to 150 of 38536 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
network_comparison
Interaction Map
green
red
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 347 1.06693 High confidence 1591.6 1491.75
484 1.06475 Low confidence 1431.5 1344.45
adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 479 1.00587 High confidence 1310.67 1318.37
505 1.05922 Low confidence 1913.73 2027.06
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 262 1.12926 High confidence 676.971 764.479
707 1.01698 Low confidence 2316.06 2355.39
adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] 35 2.99674 High confidence 1377 459.5
656 1.02537 Low confidence 2348.82 2408.41
adp-ribosylation factor 3. [swissprot;acc:p16587] 92 1.56086 High confidence 469.346 300.697
621 1.03213 Low confidence 1360.24 1403.95
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 13 29 High confidence 47 1363
490 1.06238 Low confidence 2742.78 2913.87
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 184 1.21053 19 23
195 High confidence
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 452 1.01496 1504.85 1527.36
821 1.00161 Low confidence 770.408 771.651
alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279] 179 1.21433 375.343 455.789
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 231 1.14705 High confidence 1759.22 2017.91
320 1.15942 Low confidence 1655.89 1919.88
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 266 1.1235 High confidence 1312.91 1475.05
331 1.14714 Low confidence 2382.63 2077.02
aldehyde dehydrogenase, dimeric nadp-preferring (ec 1.2.1.5) (aldh class 3) (aldhiii). [swissprot;acc:p30838] 538 1.05457 1224.9 1161.52
aldo-keto reductase family 1 member c2 (ec 1.1.1.-) (trans-1,2- dihydrobenzene-1,2-diol dehydrogenase) (ec 1.3.1.20) (chlordecone reductase homolog hakrd) (dihydrodiol dehydrogenase/bile acid-binding protein) (dd/babp) (dihydrodiol dehydrogenase 2) (dd2). [swissprot;acc:p52895] 703 1.01748 2605.86 2561.09
aldo-keto reductase family 1 member c4 (ec 1.1.1.-) (chlordecone reductase) (ec 1.1.1.225) (cdr) (3-alpha-hydroxysteroid dehydrogenase) (ec 1.1.1.50) (3-alpha-hsd) (dihydrodiol dehydrogenase 4) (dd4) (hakra). [swissprot;acc:p17516] 704 2605.82 2561.06
aldo-keto reductase loopadr; aldo-keto reductase related protein. [refseq;acc:nm_031436] 705 1.01745 2605.38 2560.7
alpha 2 globin. [refseq;acc:nm_000517] 602 1.03569 1066.67 1104.74
alpha crystallin a chain. [swissprot;acc:p02489] 86 1.61366 High confidence 89.2447 55.3059
619 1.03285 Low confidence 1749.08 1806.53
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 475 1.00722 High confidence 2335.98 2319.24
577 1.04333 Low confidence 1742.4 1817.89
alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 566 1.04919 2105.24 2208.8
571 1.04683 2308.49 2205.23
alpha-n-acetylgalactosaminidase precursor (ec 3.2.1.49) (alpha- galactosidase b). [swissprot;acc:p17050] 648 1.02674 8933.49 8700.8
alpha-nac protein. [sptrembl;acc:q9h009] 436 1.0265 High confidence 151.122 147.221
829 1.00086 Low confidence 1465.37 1464.11
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 86 1.61494 201.455 325.337
116 1.40632 High confidence 475 668
amiloride-sensitive cation channel 3 isoform a; testis sodium channel 1; proton-gated cation channel subunit; modulatory subunit of asic2a; amiloride-sensitive cation channel 3, testis. [refseq;acc:nm_004769] 139 1.29786 Low confidence 191.025 147.185
amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [swissprot;acc:p51172] 129 1.32901 194.326 146.219
amiloride-sensitive sodium channel gamma-subunit (epithelial na+ channel gamma subunit) (gamma enac) (nonvoltage-gated sodium channel 1 gamma subunit) (scneg) (gamma nach). [swissprot;acc:p51170] 140 1.29775 191.013 147.188
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 332 1.08783 High confidence 14167 15411.3
758 1.01185 Low confidence 4624.67 4679.45
anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] 62 2.09222 4356 2082
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 276 1.12092 High confidence 12125.1 10817.1
650 1.02656 Low confidence 2283.84 2224.76
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 164 1.26383 High confidence 1354.26 1711.55
351 1.13211 Low confidence 609.23 689.713
arf gtpase-activating protein. [refseq;acc:nm_133446] 74 1.78378 37 66
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 211 1.18661 High confidence 2076.5 2464
629 1.02994 Low confidence 4967.68 5116.41

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/