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 6208 to 6257 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
776 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Rooted Divided 59.6869 63.6262 1.066
777 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Squared Subtracted 25492.1 29535.4 4043.3
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Measured Divided 5874.74 6533.34 1.11211
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Ranked 225.989 215.53 1.04853
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Squared 33908.1 39510.9 1.16523
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Ranked Subtracted 221.965 212.404 9.561
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Rooted 59.7414 63.909 4.1676
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Divided 59.6869 63.6262 1.066
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Measured Subtracted 5317.78 5944.25 626.47
778 14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] Squared 28600.9 32641.7 4040.8
beta-catenin (pro2286). [swissprot;acc:p35222] Ranked 224.445 214.894 9.551
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Squared Divided 32174 37487.2 1.16514
pp1201 protein. [refseq;acc:nm_022152] Measured Subtracted 5317.78 5944.25 626.47
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Rooted 63.8039 67.9633 4.1594
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Ranked Divided 209.191 219.332 1.04848
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Rooted 59.6869 63.6262 1.066
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Measured 5874.63 6533.23 1.11211
779 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Squared Subtracted 25498.1 29537.7 4039.6
ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Rooted 57.0263 61.1552 4.1289
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Ranked Divided 230.516 241.641 1.04826
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Measured 5874.76 6533.36 1.11211
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 5317.78 5944.25 626.47
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Ranked 231.734 222.222 9.512
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Squared Divided 32174 37487.2 1.16514
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Rooted 59.6869 63.6262 1.066
780 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 57.0263 61.1552 4.1289
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Ranked Divided 232.762 243.933 1.04799
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Subtracted 231.734 222.222 9.512
phosducin-like protein (phlp). [swissprot;acc:q13371] Rooted Divided 62.2361 58.3858 1.06595
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Squared Subtracted 24818.5 28857.3 4038.8
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Measured 5317.78 5944.25 626.47
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Squared Divided 32174 37487.2 1.16514
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Measured 5874.76 6533.36 1.11211
781 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Ranked Subtracted 231.734 222.222 9.512
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Rooted 58.3914 62.5196 4.1282
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Squared 24418 28453.7 4035.7
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Rooted Divided 62.2361 58.3858 1.06595
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Ranked 245.84 257.636 1.04798
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Measured 5874.76 6533.36 1.11211
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Subtracted 5317.78 5944.25 626.47
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Squared Divided 33900.6 39498 1.16511
782 fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Subtracted 24418 28453.7 4035.7
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 33893.6 39486.1 1.165
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Ranked Subtracted 231.734 222.222 9.512
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Rooted Divided 62.2361 58.3858 1.06595
sr rich protein. [refseq;acc:nm_032870] Subtracted 61.4809 65.6088 4.1279
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Measured 6324.31 6948.5 624.19
translin. [swissprot;acc:q15631] Ranked Divided 224.385 235.131 1.04789
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Measured 5874.74 6533.33 1.11211
783 60s ribosomal protein l8. [swissprot;acc:p25120] Ranked Subtracted 231.734 222.222 9.512

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/