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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 16530 to 16579 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
2067 Measured 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 3602.75 3411.18 1.05616
Ranked adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] 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
Squared 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] 15001.4 16951.5 1950.1
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Divided 24225.6 26399 1.08972
Rooted conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Subtracted 59.3823 61.0094 1.6271
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Divided 66.6886 68.4366 1.02621
2068 Measured hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted 5391.27 5706.64 315.37
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Divided 3602.75 3411.17 1.05616
Ranked fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] 220.8 222.61 1.0082
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 207.638 205.923 1.715
Squared arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Divided 24225.6 26399 1.08972
bystin. [swissprot;acc:q13895] Subtracted 16837.1 18786.1 1949
Rooted ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Divided 59.5914 61.1533 1.02621
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Subtracted 59.3823 61.0094 1.6271
2069 Measured dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Divided 4632.65 4892.66 1.05613
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 5391.27 5706.64 315.37
Ranked 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] Divided 217.555 215.807 1.0081
fidgetin-like 1. [refseq;acc:nm_022116] Subtracted 215.511 213.814 1.697
Squared bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 23062.1 25005.1 1943
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Divided 24225.6 26399 1.08972
Rooted nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] 55.9946 57.4614 1.0262
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Subtracted 59.3823 61.0094 1.6271
2070 Measured hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] 5391.27 5706.64 315.37
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] Divided 10178.5 9638.08 1.05607
Ranked maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Subtracted 218.124 216.433 1.691
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Divided 223.199 225.008 1.0081
Squared actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] 24225.6 26399 1.08972
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted 16038 17973.3 1935.3
Rooted actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] 59.3823 61.0094 1.6271
polybromo 1. [refseq;acc:nm_018165] Divided 61.089 62.6862 1.02615
2071 Measured 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 6437.24 6797.24 1.05592
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Subtracted 5859.1 6173.7 314.6
Ranked adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 199.928 198.24 1.688
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Divided 217.555 215.807 1.0081
Squared arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] 24225.6 26399 1.08972
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Subtracted 15565.5 17500.6 1935.1
Rooted arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] 59.3823 61.0094 1.6271
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Divided 61.089 62.6862 1.02615
2072 Measured enhancer of rudimentary homolog. [swissprot;acc:q14259] 6437.24 6797.24 1.05592
oxidation resistance 1. [refseq;acc:nm_181354] Subtracted 5859.1 6173.7 314.6
Ranked 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] Divided 217.555 215.807 1.0081
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Subtracted 199.928 198.24 1.688
Squared nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Divided 24225.6 26399 1.08972
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 17375.5 19308.1 1932.6
Rooted nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] 59.3823 61.0094 1.6271
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Divided 61.089 62.6862 1.02615
2073 Measured lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Subtracted 5859.1 6173.7 314.6
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Divided 6083.39 6423.12 1.05585
Ranked 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] Subtracted 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/