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 Network Comparison Type Value Type Interaction Map red green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 16530 to 16579 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
red
green
network_comparison
2067 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided Measured 3602.75 3411.18 1.05616
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Ranked 193.226 191.639 1.00828
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Subtracted 207.655 205.939 1.716
conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Rooted 59.3823 61.0094 1.6271
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Divided 66.6886 68.4366 1.02621
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Subtracted Squared 15001.4 16951.5 1950.1
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Divided 24225.6 26399 1.08972
2068 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
bystin. [swissprot;acc:q13895] Subtracted 16837.1 18786.1 1949
fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Divided Ranked 220.8 222.61 1.0082
hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted Measured 5391.27 5706.64 315.37
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Divided 3602.75 3411.17 1.05616
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted Ranked 207.638 205.923 1.715
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Divided Rooted 59.5914 61.1533 1.02621
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Subtracted 59.3823 61.0094 1.6271
2069 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Squared 23062.1 25005.1 1943
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Divided Measured 4632.65 4892.66 1.05613
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Ranked 217.555 215.807 1.0081
fidgetin-like 1. [refseq;acc:nm_022116] Subtracted 215.511 213.814 1.697
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Measured 5391.27 5706.64 315.37
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Divided Rooted 55.9946 57.4614 1.0262
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Squared 24225.6 26399 1.08972
Subtracted Rooted 59.3823 61.0094 1.6271
2070 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] Divided Squared 24225.6 26399 1.08972
Subtracted Rooted 59.3823 61.0094 1.6271
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Measured 5391.27 5706.64 315.37
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Ranked 218.124 216.433 1.691
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Squared 16038 17973.3 1935.3
polybromo 1. [refseq;acc:nm_018165] Divided Rooted 61.089 62.6862 1.02615
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Ranked 223.199 225.008 1.0081
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Measured 10178.5 9638.08 1.05607
2071 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 6437.24 6797.24 1.05592
adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] Subtracted Ranked 199.928 198.24 1.688
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Divided Squared 24225.6 26399 1.08972
Subtracted Rooted 59.3823 61.0094 1.6271
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Squared 15565.5 17500.6 1935.1
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Measured 5859.1 6173.7 314.6
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Divided Ranked 217.555 215.807 1.0081
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Rooted 61.089 62.6862 1.02615
2072 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Ranked 217.555 215.807 1.0081
enhancer of rudimentary homolog. [swissprot;acc:q14259] Measured 6437.24 6797.24 1.05592
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Squared 24225.6 26399 1.08972
Subtracted Rooted 59.3823 61.0094 1.6271
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Ranked 199.928 198.24 1.688
oxidation resistance 1. [refseq;acc:nm_181354] Measured 5859.1 6173.7 314.6
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Divided Rooted 61.089 62.6862 1.02615
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted Squared 17375.5 19308.1 1932.6
2073 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Divided 24225.6 26399 1.08972
Subtracted Rooted 59.3823 61.0094 1.6271
adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] Ranked 199.928 198.24 1.688

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/