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 4108 to 4157 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2054 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Divided 207.665 205.948 1.00834
2055 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] Subtracted 217.555 215.807 1.748
dymeclin. [refseq;acc:nm_017653] Divided 218.79 216.981 1.00834
2056 sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Subtracted 217.555 215.807 1.748
2057 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]
lats homolog 1. [refseq;acc:nm_004690] Divided 218.79 216.981 1.00834
2058 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Subtracted 222.548 224.293 1.745
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Divided 218.79 216.981 1.00834
2059 isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] Subtracted 222.58 224.32 1.74
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Divided 218.79 216.981 1.00834
2060 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] Subtracted 222.58 224.32 1.74
2061 isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553]
tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] Divided 218.79 216.981 1.00834
2062 polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Subtracted 229.266 227.53 1.736
tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Divided 218.79 216.981 1.00834
2063 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] Subtracted 222.609 224.344 1.735
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Divided 207.638 205.923 1.00833
2064 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 207.655 205.939
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Subtracted 216.324 214.599 1.725
2065 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 207.667 205.95 1.717
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Divided 214.328 212.561 1.00831
2066 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Subtracted 207.665 205.948 1.717
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Divided 229.102 231.001 1.00829
2067 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
2068 fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Divided 220.8 222.61 1.0082
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 207.638 205.923 1.715
2069 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
2070 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 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
2071 adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] Subtracted 199.928 198.24 1.688
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Divided 217.555 215.807 1.0081
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]
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Subtracted 199.928 198.24 1.688
2073 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]
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Divided 229.267 227.433 1.00806
2074 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 216.324 214.599 1.00804
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Subtracted 215.967 214.28 1.687
2075 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Divided 221.703 223.483 1.00803
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Subtracted 215.967 214.28 1.687
2076 dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Divided 221.703 223.483 1.00803
2077 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Subtracted 215.967 214.28 1.687
2078 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668 1.681
fidgetin-like 1. [refseq;acc:nm_022116] Divided 215.511 213.814 1.00794
2079 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] 215.967 214.28 1.00787

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/