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 5508 to 5557 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1377 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Squared 22386.1 25153.7 1.12363
1378 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Rooted 61.9843 64.4891 1.04041
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Squared 22386.1 25153.7 1.12363
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Ranked 218.47 213.876 1.02148
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Measured 6079.45 6555.4 1.07829
1379 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Ranked 218.47 213.875 1.02148
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Rooted 61.9865 64.4916 1.04041
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Measured 6079.46 6555.41 1.07829
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Squared 22386.1 25153.7 1.12363
1380 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Measured 6079.46 6555.41 1.07829
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] Rooted 61.9842 64.489 1.04041
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Squared 22386.1 25153.7 1.12363
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Ranked 218.47 213.876 1.02148
1381 glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Measured 6079.46 6555.41 1.07829
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Squared 29952.7 33648.1 1.12337
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942] Rooted 61.986 64.4911 1.04041
rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Ranked 218.47 213.876 1.02148
1382 histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Measured 6079.46 6555.41 1.07829
nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384] Rooted 63.1214 65.6707 1.04039
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Ranked 218.47 213.876 1.02148
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Squared 29952.7 33648.1 1.12337
1383 adaptor-associated kinase 1. [refseq;acc:nm_014911] Ranked 218.47 213.876 1.02148
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Rooted 53.5945 51.5157 1.04035
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Squared 20766.9 23326.7 1.12326
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Measured 6079.45 6555.4 1.07829
1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Ranked 218.471 213.876 1.02148
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Squared 25044.6 28129.1 1.12316
immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] Rooted 60.7706 63.219 1.04029
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] Measured 6079.45 6555.4 1.07829
1385 calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7]
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Squared 19622 22037.7 1.12311
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Ranked 218.47 213.875 1.02148
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Rooted 60.9624 63.4098 1.04015
1386 calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] Measured 6079.46 6555.41 1.07829
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Squared 19367.8 21747.4 1.12286
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Rooted 60.9624 63.4098 1.04015
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Ranked 218.47 213.876 1.02148
1387 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] Squared 19336.4 21711.3 1.12282
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] Measured 6079.46 6555.4 1.07829
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Rooted 60.3917 62.8083 1.04002
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Ranked 218.47 213.875 1.02148
1388 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Rooted 60.9652 63.4052 1.04002
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Squared 18314.2 20563 1.12279
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Measured 5743.39 6192.94 1.07827
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Ranked 218.471 213.876 1.02148
1389 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 218.47 213.875
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Rooted 93.3148 89.7311 1.03994
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] Measured 6079.13 6554.85 1.07825
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Squared 18314.2 20563 1.12279
1390 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Ranked 218.47 213.875 1.02148

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/