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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6708 to 6757 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1677 ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Measured 6075.19 6496.61 1.06937
1678 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] 5763.25 6162.98 1.06936
heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] Squared 26940.8 29785.9 1.10561
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Rooted 60.3002 62.3124 1.03337
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Ranked 216.899 213.889 1.01407
1679 gtp binding protein 2. [refseq;acc:nm_019096]
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Rooted 56.5094 58.3923 1.03332
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Measured 6180.24 6608.11 1.06923
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Squared 31163.9 34454.3 1.10558
1680 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933]
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Ranked 216.899 213.889 1.01407
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Measured 6436.73 6882.16 1.0692
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Rooted 56.5094 58.3923 1.03332
1681 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Ranked 216.899 213.889 1.01407
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Measured 6304.74 6740.66 1.06914
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Squared 31163.9 34454.3 1.10558
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Rooted 56.5094 58.3923 1.03332
1682 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Measured 6304.74 6740.66 1.06914
glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Squared 31163.9 34454.3 1.10558
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Ranked 216.899 213.889 1.01407
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Rooted 56.5094 58.3923 1.03332
1683 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] Ranked 216.899 213.889 1.01407
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Squared 25120.7 27772.9 1.10558
ring finger protein 20. [refseq;acc:nm_019592] Measured 5419.54 5793.94 1.06908
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Rooted 56.5094 58.3923 1.03332
1684 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Squared 27060.6 29916.8 1.10555
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Rooted 56.5094 58.3923 1.03332
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Measured 5419.54 5793.94 1.06908
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Ranked 216.899 213.889 1.01407
1685 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Squared 27060.6 29916.8 1.10555
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Measured 6088.07 6508.45 1.06905
homeobox protein dlx-2. [swissprot;acc:q07687] Rooted 56.5094 58.3923 1.03332
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Ranked 216.899 213.889 1.01407
1686 dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Squared 27060.6 29916.8 1.10555
homeobox protein dlx-5. [swissprot;acc:p56178] Rooted 56.5094 58.3923 1.03332
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Ranked 220.75 217.704 1.01399
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Measured 6088.07 6508.45 1.06905
1687 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Squared 27060.6 29916.8 1.10555
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Ranked 215.345 212.386 1.01393
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Rooted 56.5094 58.3923 1.03332
serpin b12. [swissprot;acc:q96p63] Measured 5767.69 6165.87 1.06904
1688 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Squared 27060.6 29916.8 1.10555
homeobox protein dlx-3. [swissprot;acc:o60479] Rooted 56.5094 58.3923 1.03332
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Measured 5767.69 6165.87 1.06904
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Ranked 228.523 231.703 1.01392
1689 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Rooted 56.5094 58.3923 1.03332
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Squared 27060.6 29916.8 1.10555
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Ranked 228.277 225.163 1.01383
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Measured 5767.69 6165.87 1.06904
1690 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Ranked 224.091 227.184 1.0138

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/