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 3080 to 3129 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
770 vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Measured 5874.74 6533.34 1.11211
771 40s ribosomal protein s19. [swissprot;acc:p39019] Rooted 55.6817 59.3786 1.06639
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] Measured 5874.74 6533.34 1.11211
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Ranked 210.946 221.225 1.04873
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Squared 24418 28453.7 1.16528
772 60s ribosomal protein l31. [swissprot;acc:p12947] Rooted 55.6817 59.3786 1.06639
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Ranked 210.946 221.225 1.04873
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Squared 24418 28453.7 1.16528
sec13-related protein. [swissprot;acc:p55735] Measured 5874.76 6533.36 1.11211
773 coactosin-like protein. [swissprot;acc:q14019] Squared 24418 28453.7 1.16528
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Rooted 127.967 120.003 1.06637
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Ranked 210.946 221.225 1.04873
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Measured 5874.74 6533.34 1.11211
774 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Rooted 65.3248 69.648 1.06618
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Ranked 225.996 215.535 1.04854
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Squared 24418 28453.7 1.16528
yeast sec31p homolog. [refseq;acc:nm_014933] Measured 5874.76 6533.36 1.11211
775 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Rooted 62.2385 58.38 1.06609
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Ranked 226.003 215.541 1.04854
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Squared 24418 28453.7 1.16528
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Measured 5874.74 6533.33 1.11211
776 40s ribosomal protein s13. [swissprot;acc:q02546] Squared 21976 25607.9 1.16527
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked 225.996 215.535 1.04854
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Measured 5874.76 6533.36 1.11211
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Rooted 59.6869 63.6262 1.066
777 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Measured 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
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Rooted 59.6869 63.6262 1.066
778 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Squared 32174 37487.2 1.16514
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Ranked 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 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Ranked 230.516 241.641 1.04826
ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Measured 5874.76 6533.36 1.11211
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Squared 32174 37487.2 1.16514
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Rooted 59.6869 63.6262 1.066
780 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Ranked 232.762 243.933 1.04799
phosducin-like protein (phlp). [swissprot;acc:q13371] Rooted 62.2361 58.3858 1.06595
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Squared 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 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 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
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Squared 33900.6 39498 1.16511
782 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 33893.6 39486.1 1.165
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Rooted 62.2361 58.3858 1.06595
translin. [swissprot;acc:q15631] Ranked 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 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared 27407.7 31927.7 1.16492

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/