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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Network Comparison Type Gene red Value Type Rank green Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1368 to 1417 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
Rank
green
description
network_comparison
5384.41 724 6012.82 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 1.11671
725 phenylalanine-trna synthetase. [refseq;acc:nm_006567]
5384.89 1750 5746.51 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] 1.06715
5385.04 891 5933.65 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 1.10188
5386.37 1774 5744.89 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 1.06656
1775 zinc finger protein 258. [refseq;acc:nm_145310]
1776 zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
1777 zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
1778 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
1779 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
1780 similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
1781 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
1782 zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
1783 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
1784 arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
1785 nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
1786 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
5386.48 1787 5744.78 interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] 1.06652
5386.49 1788 5744.76 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] 1.06651
5387.64 1796 5743.5 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] 1.06605
5390.78 521 6142.07 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 1.13937
5391.27 2011 5706.64 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 1.0585
2012 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839]
2013 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219]
5391.64 1004 5903.72 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] 1.09498
5393.37 992 5909.47 putative sialoglycoprotease type 2. [refseq;acc:nm_022353] 1.09569
5394.24 1918 5730.73 seven in absentia homolog 1. [refseq;acc:nm_003031] 1.06238
5396.36 919 5929.41 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 1.09878
5396.61 1906 5733.93 mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] 1.06251
5397.21 1547 5790.45 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 1.07286
5399.47 1900 5737.79 seven in absentia homolog 2. [refseq;acc:nm_005067] 1.06266
5401.39 1314 5838.63 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] 1.08095
5406.5 924 5939.42 opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] 1.09857
5412.23 1057 5913.4 tata element modulatory factor (tmf). [swissprot;acc:p82094] 1.0926
1058 scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]
1061 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
1062 ammecr1 protein. [refseq;acc:nm_015365]
1063 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]
5413.63 935 5946.46 neurotrimin precursor (hnt). [swissprot;acc:q9p121] 1.09842
5414.98 1498 5818.7 40s ribosomal protein s13. [swissprot;acc:q02546] 1.07456
5417.06 1066 5917.79 leucyl-trna synthetase. [refseq;acc:nm_020117] 1.09244
5417.07 1067 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 1.09243
5417.95 1038 5924.41 myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] 1.09348
5418.33 1157 5895.2 serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 1.08801
5418.92 1039 5923.09 myb-related protein b (b-myb). [swissprot;acc:p10244] 1.09304
5419.18 1041 5922.84 myb-related protein a (a-myb). [swissprot;acc:p10243] 1.09294
5419.54 1683 5793.94 ring finger protein 20. [refseq;acc:nm_019592] 1.06908
1684 ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]
5420.87 1209 5887.53 bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 1.08609
5421.93 1040 5926.08 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 1.09298

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/