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 3477 to 3526 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1739 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Divided 5695.57 6079.61 1.06743
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Subtracted 5369.1 5763.72 394.62
1740 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 5948.26 6342.84 394.58
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Divided 5878.2 6274.27 1.06738
1741 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Subtracted 4935.58 5329.93 394.35
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Divided 6297.05 6721.08 1.06734
1742 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] Subtracted 6104.77 6498.84 394.07
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Divided 6298.76 6722.61 1.06729
1743 histidine-rich membrane protein ke4. [swissprot;acc:q92504] 6298.81 6722.65
protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] Subtracted 6158.6 6551.94 393.34
1744 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 5397.21 5790.45 393.24
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Divided 6298.81 6722.65 1.06729
1745 adenovirus 5 e1a-binding protein (bs69 protein). [swissprot;acc:q15326] Subtracted 6156.28 6549.03 392.75
microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Divided 6298.77 6722.62 1.06729
1746 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Subtracted 5117.85 5510.45 392.6
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Divided 5683.17 6065.55 1.06728
1747 cerebral cell adhesion molecule. [refseq;acc:nm_016174] 9596.59 10241.9 1.06724
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Subtracted 5117.85 5510.45 392.6
1748 doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] Divided 6301.03 6724.63 1.06723
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Subtracted 5117.85 5510.45 392.6
1749 electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Divided 7919.76 8452.01 1.06721
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Subtracted 5520.36 5911.98 391.62
1750 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Divided 5384.89 5746.51 1.06715
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Subtracted 5781.8 6173.1 391.3
1751 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] Divided 6011.57 6414.98 1.06711
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Subtracted 6262.66 6652.85 390.19
1752 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Divided 5941.29 6339.93 1.0671
salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [swissprot;acc:p10162] Subtracted 6262.66 6652.85 390.19
1753 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Divided 5423.67 5787.46 1.06707
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Subtracted 5283.8 5673.81 390.01
1754 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Divided 5941.83 6340.32 1.06707
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Subtracted 5283.8 5673.81 390.01
1755 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 6766.45 7155.54 389.09
chromodomain y-like protein 2. [refseq;acc:nm_152342] Divided 7101.7 7577.75 1.06703
1756 40s ribosomal protein s29. [swissprot;acc:p30054] 3582.57 3357.6 1.067
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Subtracted 5829.73 6218.45 388.72
1757 beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] 5829.61 6218.27 388.66
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Divided 7101.15 7576.84 1.06699
1758 beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Subtracted 5829.61 6218.27 388.66
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Divided 7101.15 7576.84 1.06699
1759 nitrilase 1. [refseq;acc:nm_005600] Subtracted 5829.61 6218.27 388.66
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Divided 7101.16 7576.87 1.06699
1760 thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] 5693.88 6075.25 1.06698
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Subtracted 5829.61 6218.27 388.66
1761 electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Divided 7794.41 8316.04 1.06692
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Subtracted 5829.61 6218.27 388.66
1762 dystrophin. [swissprot;acc:p11532]
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Divided 6122.76 6531.3 1.06672
1763 angiomotin. [refseq;acc:nm_133265] Subtracted 5829.61 6218.27 388.66
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Divided 5829.73 6218.45 1.06668

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/