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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3075 to 3124 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
769 Squared n-acetylglutamate synthase. [refseq;acc:nm_153006] 20943 24412.8 1.16568
Rooted 60s ribosomal protein l39. [swissprot;acc:p02404] 55.6817 59.3786 1.06639
770 Measured 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] 5874.74 6533.34 1.11211
Ranked dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] 210.946 221.225 1.04873
Squared fibulin-2 precursor. [swissprot;acc:p98095] 45189.6 52666.2 1.16545
Rooted 60s ribosomal protein l18a. [swissprot;acc:q02543] 55.6817 59.3786 1.06639
771 Measured apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 5874.74 6533.34 1.11211
Ranked 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] 210.946 221.225 1.04873
Squared glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] 24418 28453.7 1.16528
Rooted 40s ribosomal protein s19. [swissprot;acc:p39019] 55.6817 59.3786 1.06639
772 Measured sec13-related protein. [swissprot;acc:p55735] 5874.76 6533.36 1.11211
Ranked eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] 210.946 221.225 1.04873
Squared fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] 24418 28453.7 1.16528
Rooted 60s ribosomal protein l31. [swissprot;acc:p12947] 55.6817 59.3786 1.06639
773 Measured 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] 5874.74 6533.34 1.11211
Ranked suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] 210.946 221.225 1.04873
Squared coactosin-like protein. [swissprot;acc:q14019] 24418 28453.7 1.16528
Rooted serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] 127.967 120.003 1.06637
774 Measured yeast sec31p homolog. [refseq;acc:nm_014933] 5874.76 6533.36 1.11211
Ranked multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
Squared uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] 24418 28453.7 1.16528
Rooted 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] 65.3248 69.648 1.06618
775 Measured 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] 5874.74 6533.33 1.11211
Ranked histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541 1.04854
Squared 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] 24418 28453.7 1.16528
Rooted clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 62.2385 58.38 1.06609
776 Measured ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 5874.76 6533.36 1.11211
Ranked dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 225.996 215.535 1.04854
Squared 40s ribosomal protein s13. [swissprot;acc:q02546] 21976 25607.9 1.16527
Rooted sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 59.6869 63.6262 1.066
777 Measured dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 5874.74 6533.34 1.11211
Ranked histone deacetylase 1 (hd1). [swissprot;acc:q13547] 225.989 215.53 1.04853
Squared importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 33908.1 39510.9 1.16523
Rooted sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 59.6869 63.6262 1.066
778 Measured 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] 5874.63 6533.23 1.11211
Ranked sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
Squared mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 32174 37487.2 1.16514
Rooted sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 59.6869 63.6262 1.066
779 Measured ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36 1.11211
Ranked deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 230.516 241.641 1.04826
Squared probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 32174 37487.2 1.16514
Rooted sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 59.6869 63.6262 1.066
780 Measured 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] 5874.76 6533.36 1.11211
Ranked dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 232.762 243.933 1.04799
Squared tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] 32174 37487.2 1.16514
Rooted phosducin-like protein (phlp). [swissprot;acc:q13371] 62.2361 58.3858 1.06595
781 Measured secretory pathway component sec31b-1. [refseq;acc:nm_015490] 5874.76 6533.36 1.11211
Ranked ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] 245.84 257.636 1.04798
Squared target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 33900.6 39498 1.16511
Rooted 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] 62.2361 58.3858 1.06595

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/