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 3208 to 3257 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1604 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Subtracted 6260.43 6685.05 424.62
1605 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Divided 6176.82 6617.91 1.07141
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Subtracted 6259.8 6684.31 424.51
1606 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Divided 5232.99 5606.53 1.07138
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Subtracted 6259.8 6684.3 424.5
1607 putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Divided 5232.99 5606.53 1.07138
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 4379.28 4803.59 424.31
1608 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 7019.78 7444.06 424.28
ubiquitin. [swissprot;acc:p02248] Divided 6158.22 6597.55 1.07134
1609 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Subtracted 6297.05 6721.08 424.03
1610 eif-5a2 protein. [refseq;acc:nm_020390] Divided 6222.4 6665.83 1.07126
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Subtracted 6079.19 6503.12 423.93
1611 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Divided 5497.73 5132.35 1.07119
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Subtracted 6079.19 6503.12 423.93
1612 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] Divided 6212.98 6655.12 1.07116
1613 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Subtracted 6079.19 6503.12 423.93
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Divided 6035.6 6464.5 1.07106
1614 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Subtracted 6079.19 6503.12 423.93
1615 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Divided 6035.6 6464.5 1.07106
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Subtracted 6079.19 6503.12 423.93
1616 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 4078.45 4502.32 423.87
mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Divided 6035.6 6464.5 1.07106
1617 lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663]
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Subtracted 6298.76 6722.61 423.85
1618 microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] 6298.77 6722.62
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] Divided 6035.6 6464.5 1.07106
1619 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Subtracted 6298.81 6722.65 423.84
1620 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Divided 6296.52 6743.85 1.07104
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Subtracted 6298.81 6722.65 423.84
1621 doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] 6301.03 6724.63 423.6
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Divided 5520.36 5911.98 1.07094
1622 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] Subtracted 5783.97 6207.5 423.53
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Divided 6153.79 6589.52 1.07081
1623 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Subtracted 5846.67 6269.41 422.74
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Divided 6449.02 6905.56 1.07079
1624 protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Subtracted 5845.22 6267.34 422.12
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Divided 4102.1 4392.15 1.07071
1625 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Subtracted 5851.64 6273.4 421.76
zinc finger protein 277. [swissprot;acc:q9nrm2] Divided 4102.1 4392.15 1.07071
1626 phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] 6157.13 6591.53 1.07055
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Subtracted 6075.19 6496.61 421.42
1627 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 6038.46 6463.9 1.07046
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Subtracted 4076.72 4497.74 421.02
1628 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 5822.25 6242.94 420.69
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Divided 5920.55 6337.28 1.07039
1629 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] 6158.32 6590.99 1.07026

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/