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 12314 to 12363 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1540 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Ranked Divided 240.077 236.015 1.01721
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Rooted 63.304 65.6156 1.03652
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Measured 6360.13 6825.36 1.07315
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Squared Subtracted 21776.6 24369.1 2592.5
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Rooted 63.8754 66.1935 2.3181
pxr2b protein. [refseq;acc:nm_016559] Measured 6996.51 7429.18 432.67
translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10] Squared Divided 23482.8 26128.5 1.11267
1541 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 26551.2 29539 1.11253
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] Rooted Subtracted 63.9658 66.2831 2.3173
adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Measured Divided 5989.3 6427.17 1.07311
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Subtracted 6158.32 6590.99 432.67
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Ranked 192.336 188.637 3.699
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Rooted Divided 63.3022 65.6127 1.0365
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Ranked 222.672 218.92 1.01714
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Squared Subtracted 19239.8 21829.3 2589.5
1542 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Measured 5686.74 6119.36 432.62
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Squared Divided 2557.92 2299.4 1.11243
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Measured 5466 5865.33 1.07306
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Ranked Subtracted 219.762 216.081 3.681
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Squared 26990.9 29579.6 2588.7
symplekin. [swissprot;acc:q92797] Rooted Divided 99.9862 96.4662 1.03649
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Ranked 213.546 209.965 1.01706
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Rooted Subtracted 64.5089 66.8255 2.3166
1543 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Measured 6885.11 7317.48 432.37
afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Divided 5466 5865.33 1.07306
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Ranked 213.546 209.965 1.01706
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Squared 2558.19 2299.7 1.1124
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 27812.9 30401.4 2588.5
orphan nuclear receptor tr2. [swissprot;acc:p13056] Ranked 219.76 216.083 3.677
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Rooted Divided 64.2792 66.6225 1.03646
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 64.7716 67.0877 2.3161
1544 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Measured Divided 5466 5865.33 1.07306
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Squared 18161.1 20200 1.11227
hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Measured Subtracted 5798.31 6230.55 432.24
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Ranked Divided 219.762 216.081 1.01704
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Rooted 76.2612 79.0401 1.03644
tax interaction protein 1. [refseq;acc:nm_014604] Squared Subtracted 27812.9 30401.4 2588.5
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Ranked 225.119 228.769 3.65
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Rooted 64.5103 66.8259 2.3156
1545 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Measured Divided 5945.96 6380.28 1.07304
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Ranked Subtracted 225.119 228.769 3.65
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Squared 24923.8 27509.9 2586.1
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Measured 5672.68 6104.68 432
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Rooted 60.3017 62.6158 2.3141
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Squared Divided 18159.2 20197.6 1.11225
orphan nuclear receptor tr2. [swissprot;acc:p13056] Ranked 219.76 216.083 1.01702
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Rooted 76.2612 79.0401 1.03644
1546 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Measured 5819.39 6244.37 1.07303
60s ribosomal protein l15. [swissprot;acc:p39030] Squared Subtracted 17766.4 20351.7 2585.3
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Ranked Divided 217.769 221.474 1.01701

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/