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 11264 to 11313 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1408 topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Squared Subtracted 19141.8 21912.9 2771.1
1409 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Divided 21512.7 24115.7 1.121
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Subtracted 31411.4 34180.5 2769.1
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] Measured Divided 5358.19 5773.37 1.07749
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Rooted 65.3456 67.9119 1.03927
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Measured Subtracted 6221.35 6672.51 451.16
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Rooted 62.3815 64.865 2.4835
trap/mediator complex component trap25. [refseq;acc:nm_080651] Ranked Divided 206.102 210.42 1.02095
Subtracted 4.318
1410 delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Measured Divided 6274.62 6760.78 1.07748
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Rooted 65.3456 67.9119 1.03927
leng5 protein. [refseq;acc:nm_024075] Squared Subtracted 22386.1 25153.7 2767.6
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Divided 17102.5 19171.7 1.12099
rna (guanine-7-) methyltransferase. [refseq;acc:nm_003799] Rooted Subtracted 62.3815 64.865 2.4835
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Ranked 206.102 210.42 4.318
transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354] Measured 7260.23 7711.3 451.07
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Ranked Divided 206.1 210.417 1.02095
1411 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Measured 5812.02 6262.07 1.07743
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Rooted Subtracted 53.3231 50.8416 2.4815
frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] Measured 7260.23 7711.3 451.07
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Rooted Divided 65.3456 67.9119 1.03927
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Squared 8107.35 9087.76 1.12093
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Ranked Subtracted 206.102 210.42 4.318
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Divided 1.02095
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Squared Subtracted 22386.1 25153.7 2767.6
1412 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Ranked 206.102 210.42 4.318
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Rooted Divided 65.3456 67.9119 1.03927
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Measured 5813.84 6263.92 1.07742
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Ranked 206.102 210.42 1.02095
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Squared Subtracted 22386.1 25153.7 2767.6
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Rooted 59.8171 62.2984 2.4813
transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478] Measured 7260.23 7711.3 451.07
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Squared Divided 22981.1 25758.4 1.12085
1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Ranked 206.102 210.42 1.02095
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] Measured Subtracted 7260.23 7711.29 451.06
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Divided 5813.88 6263.97 1.07742
homolog of yeast maf1. [refseq;acc:nm_032272] Rooted 65 67.552 1.03926
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Subtracted 59.8171 62.2984 2.4813
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Ranked 206.102 210.42 4.318
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Squared Divided 22981.1 25758.4 1.12085
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Subtracted 22386.1 25153.7 2767.6
1414 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Measured 5984.47 6435.42 450.95
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Divided 5813.88 6263.96 1.07741
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Rooted Subtracted 57.8563 55.3779 2.4784
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Ranked Divided 206.102 210.42 1.02095
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Subtracted 4.318
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Squared 22386.1 25153.7 2767.6
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Rooted Divided 65 67.552 1.03926
uridine kinase-like 1. [swissprot;acc:q9nwz5] Squared 24302 27238.6 1.12084
1415 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Measured 5815.33 6265.44 1.0774

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/