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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Gene description Value Type Filtered Rank Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 501 to 550 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
description
Filtered
Rank
network_comparison
Interaction Map
green
red
actin-related protein 6 (harp6) (harpx) (cda12). [swissprot;acc:q9gzn1] 1 3049 1.0166 Low confidence 196.826 200.094
actin-related protein 8. [swissprot;acc:q9h981] 4788 1.00435 213.795 212.869
activated p21cdc42hs kinase. [refseq;acc:nm_005781] 493 1.03288 202.478 209.136
2341 1.00452 High confidence 230.294 229.258
activated rna polymerase ii transcriptional coactivator p15 (pc4) (p14). [swissprot;acc:p53999] 3118 1.01641 Low confidence 198.391 201.646
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] 2771 1.01742 197.788 201.233
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] 1169 1.02626 High confidence 213.784 219.399
2633 1.01778 Low confidence 199.198 202.74
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482] 1303 1.02368 High confidence 275.531 269.157
4902 1.00197 Low confidence 208.323 208.733
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 1257 1.02259 199.543 204.05
1366 1.02194 High confidence 228.795 223.884
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] 2874 1.01711 Low confidence 200.634 204.066
3050 1 High confidence 0.00001 0.00001
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] 2498 1.00284 195.08 194.527
2823 1.01725 Low confidence 193.252 196.586
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] 1413 1.02095 High confidence 210.42 206.102
1757 1.02029 Low confidence 198.864 202.898
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] 0 105 1.21243 High confidence 14360 17410.5
655 1.02356 Low confidence 14410 14078.3
1 2019 1.00904 High confidence 213.865 215.799
3051 1.01659 Low confidence 199.311 202.617
acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 733 1.05154 High confidence 155.961 164
853 1.02582 Low confidence 194.759 199.788
acyl-coa desaturase (ec 1.14.19.1) (stearoyl-coa desaturase) (fatty acid desaturase) (delta(9)-desaturase). [swissprot;acc:o00767] 4723 1.00555 195.824 196.91
acyl-coa-binding protein (acbp) (diazepam binding inhibitor) (dbi) (endozepine) (ep). [swissprot;acc:p07108] 1698 1.02056 197.873 201.941
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] 1697
2643 1.00119 High confidence 194.328 194.097
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] 2404 1.0037 194.105 193.389
2754 1.01745 Low confidence 193.162 196.532
acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254] 3892 1.01271 197.485 199.996
ad-003 protein. [refseq;acc:nm_014064] 3670 1.0139 200.281 203.065
ad023 protein. [refseq;acc:nm_020679] 3422 1.01523 199.025 202.056
ad037 protein isoform a. [refseq;acc:nm_032023] 4059 1.01123 200.731 202.985
ad24 protein. [refseq;acc:nm_022451] 505 1.071 High confidence 234.672 251.334
947 1.02488 Low confidence 198.533 203.472
adam-ts related protein 1 isoform 1; adam-ts related protein 1; thrombospondin; punctin. [refseq;acc:nm_139238] 1620 1.02083 199.732 203.893
adam-tsl3 precursor (fragment). [sptrembl;acc:p82987] 1623 1.0208 199.748 203.903
adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] 2481 1.01825 199.724 203.369
2516 1.00234 High confidence 216.341 215.835
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] 458 1.03444 Low confidence 200.058 206.948
1586 1.01631 High confidence 225.79 222.166
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] 416 1.03545 Low confidence 200.339 207.442
1596 1.01619 High confidence 225.731 222.134
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 408 1.03591 Low confidence 200.363 207.558
1594 1.0162 High confidence 225.731 222.133
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] 699 1.0279 Low confidence 199.601 205.169
1598 1.01619 High confidence 225.731 222.134
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] 0 368 1.04633 15940.6 16679.2
565 1.04452 Low confidence 13171.2 12609.8

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/