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 Hugo description Value Type 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
Hugo
description
Value Type
red
green
network_comparison
776 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Ranked 225.996 215.535 1.04854
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Rooted 59.6869 63.6262 1.066
GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Measured 5874.76 6533.36 1.11211
RPS13 40s ribosomal protein s13. [swissprot;acc:q02546] Squared 21976 25607.9 1.16527
777 DDX39 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
HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Ranked 225.989 215.53 1.04853
KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Squared 33908.1 39510.9 1.16523
SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Rooted 59.6869 63.6262 1.066
778 ATP6V1B1 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
MAD2L1 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Squared 32174 37487.2 1.16514
SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Ranked 209.191 219.332 1.04848
SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Rooted 59.6869 63.6262 1.066
779 ATP13A2 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Squared 32174 37487.2 1.16514
DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Ranked 230.516 241.641 1.04826
GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Measured 5874.76 6533.36 1.11211
SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Rooted 59.6869 63.6262 1.066
780 ATP6V1D 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
PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] Rooted 62.2361 58.3858 1.06595
POLR2F 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
TBP 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
781 MRTO4 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
RPA1 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
SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] Measured 5874.76 6533.36 1.11211
TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Squared 33900.6 39498 1.16511
782 no value translin. [swissprot;acc:q15631] Ranked 224.385 235.131 1.04789
ATP6V1H 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
KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Squared 33893.6 39486.1 1.165
RPA2 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
783 no value hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Squared 27407.7 31927.7 1.16492
ATP6V1B2 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] Measured 5874.78 6533.37 1.1121
PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Rooted 62.2361 58.3858 1.06595
TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Ranked 224.385 235.131 1.04789
784 no value dc11 protein. [refseq;acc:nm_020186] Squared 27407.7 31927.7 1.16492
ATP6V1E1 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] Measured 5874.77 6533.36 1.1121
PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Ranked 224.385 235.131 1.04789
RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] Rooted 62.2361 58.3858 1.06595
785 APPBP1 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] Squared 27407.7 31927.7 1.16492
CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Rooted 62.2332 58.3925 1.06577
HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Measured 4997 5557.17 1.1121
NET1 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Ranked 244.447 233.508 1.04685
786 ALAS2 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Squared 27407.7 31927.7 1.16492
ARHGEF3 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] Ranked 244.447 233.508 1.04685
PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Measured 9304.83 10347.3 1.11204
RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] Rooted 52.0101 48.813 1.0655
787 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 64.5489 68.7769
ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Measured 5890.49 6547.9 1.11161
UBE1C ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Squared 27407.7 31927.7 1.16492
UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] Ranked 244.447 233.508 1.04685
788 no value ero1-like. [refseq;acc:nm_014584] Rooted 64.5489 68.7769 1.0655
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Ranked 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
- Hugo is the HGNC identifier if it exists
- 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/