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 3101 to 3150 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
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
782 Measured 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] 5874.74 6533.33 1.11211
Ranked translin. [swissprot;acc:q15631] 224.385 235.131 1.04789
Squared importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 33893.6 39486.1 1.165
Rooted replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 62.2361 58.3858 1.06595
783 Measured vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 5874.78 6533.37 1.1121
Ranked translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] 224.385 235.131 1.04789
Squared hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 27407.7 31927.7 1.16492
Rooted phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 62.2361 58.3858 1.06595
784 Measured vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] 5874.77 6533.36 1.1121
Ranked polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] 224.385 235.131 1.04789
Squared dc11 protein. [refseq;acc:nm_020186] 27407.7 31927.7 1.16492
Rooted dna repair protein rad52 homolog. [swissprot;acc:p43351] 62.2361 58.3858 1.06595
785 Measured hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 4997 5557.17 1.1121
Ranked neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 244.447 233.508 1.04685
Squared amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] 27407.7 31927.7 1.16492
Rooted clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 62.2332 58.3925 1.06577
786 Measured pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 9304.83 10347.3 1.11204
Ranked rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 244.447 233.508 1.04685
Squared 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 27407.7 31927.7 1.16492
Rooted 40s ribosomal protein s9. [swissprot;acc:p46781] 52.0101 48.813 1.0655
787 Measured vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 5890.49 6547.9 1.11161
Ranked down-regulated in metastasis. [refseq;acc:nm_014503] 244.447 233.508 1.04685
Squared ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] 27407.7 31927.7 1.16492
Rooted uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 64.5489 68.7769 1.0655
788 Measured vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] 5890.41 6547.81 1.11161
Ranked hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 138.705 132.538 1.04653

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/