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 501 to 550 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
Interaction Map
Filtered
red
green
network_comparison
actin-related protein 6 (harp6) (harpx) (cda12). [swissprot;acc:q9gzn1] 4236 Low confidence 1 8224.26 8388.41 1.01996
actin-related protein 8. [swissprot;acc:q9h981] 4140 7289.4 7441.89 1.02092
activated p21cdc42hs kinase. [refseq;acc:nm_005781] 1055 High confidence 4757.46 5198.91 1.09279
2089 Low confidence 7691.09 7935.53 1.03178
activated rna polymerase ii transcriptional coactivator p15 (pc4) (p14). [swissprot;acc:p53999] 2793 8031.65 8265.89 1.02916
activator 1 140 kda subunit (replication factor c large subunit) (a1 140 kda subunit) (rf-c 140 kda subunit) (activator 1 large subunit) (dna-binding protein po-ga). [swissprot;acc:p35251] 2758 8074.81 8311.1 1.02926
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 1146 High confidence 6281.21 6837.61 1.08858
3141 Low confidence 7977.41 8196.72 1.02749
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 2435 High confidence 3669.33 3797.78 1.03501
4485 Low confidence 7667.47 7812.25 1.01888
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 2141 7890.09 8139.78 1.03165
2160 High confidence 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] 2173 Low confidence 7907.92 8157.25 1.03153
3050 High confidence 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
3446 Low confidence 8237.69 8454.36 1.0263
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] 1865 7947.06 8206.59 1.03266
2612 High confidence 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] 44 0 45.4292 98.5074 2.16837
87 Low confidence 129.715 81.6539 1.5886
1620 High confidence 1 6296.52 6743.85 1.07104
2125 Low confidence 7920.13 8171.2 1.0317
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 380 High confidence 12998.5 15138.2 1.16461
482 Low confidence 8350.58 8763.72 1.04947
acyl-coa desaturase (ec 1.14.19.1) (stearoyl-coa desaturase) (fatty acid desaturase) (delta(9)-desaturase). [swissprot;acc:o00767] 4214 7963.96 8124.86 1.0202
acyl-coa-binding protein (acbp) (diazepam binding inhibitor) (dbi) (endozepine) (ep). [swissprot;acc:p07108] 2985 7989.61 8214.14 1.0281
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] 2035 High confidence 6920.71 7315.59 1.05706
2984 Low confidence 7989.61 8214.14 1.0281
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 High confidence 6884.69 7247.36 1.05268
2842 Low confidence 8208.35 8445.14 1.02885
acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254] 3985 8124.9 8307.41 1.02246
ad-003 protein. [refseq;acc:nm_014064] 3343 7908.04 8118.72 1.02664
ad023 protein. [refseq;acc:nm_020679] 3093 8001.62 8223.41 1.02772
ad037 protein isoform a. [refseq;acc:nm_032023] 2727 7899.01 8131.4 1.02942
ad24 protein. [refseq;acc:nm_022451] 445 High confidence 3753.71 4315.95 1.14978
3097 Low confidence 7954.48 8174.68 1.02768
adam-ts related protein 1 isoform 1; adam-ts related protein 1; thrombospondin; punctin. [refseq;acc:nm_139238] 2288 7930.03 8176.98 1.03114
adam-tsl3 precursor (fragment). [sptrembl;acc:p82987] 2298 7929.54 8176.24 1.03111
adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] 1530 High confidence 5916.05 6350.53 1.07344
2177 Low confidence 7930.22 8180.02 1.0315
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] 1048 7724.96 8016.23 1.03771
2064 High confidence 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] 1158 Low confidence 7694.94 7977.35 1.0367
2059 High confidence 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] 1125 Low confidence 7688.48 7972.75 1.03697
2062 High confidence 5552.7 5865.85 1.0564
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] 1564 Low confidence 7827.75 8092.26 1.03379
2061 High confidence 5552.69 5865.84 1.0564
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] 60 0 47.4756 87.5499 1.8441
534 Low confidence 781.187 740.494 1.05495

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/