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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type Hugo 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
Hugo
description
red
green
network_comparison
776 Measured GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 5874.76 6533.36 1.11211
Ranked no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 225.996 215.535 1.04854
Squared RPS13 40s ribosomal protein s13. [swissprot;acc:q02546] 21976 25607.9 1.16527
Rooted no value sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 59.6869 63.6262 1.066
777 Measured DDX39 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 HDAC1 histone deacetylase 1 (hd1). [swissprot;acc:q13547] 225.989 215.53 1.04853
Squared KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 33908.1 39510.9 1.16523
Rooted SPRY3 sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 59.6869 63.6262 1.066
778 Measured 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] 5874.63 6533.23 1.11211
Ranked SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
Squared MAD2L1 mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] 32174 37487.2 1.16514
Rooted SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 59.6869 63.6262 1.066
779 Measured GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36 1.11211
Ranked DCTD deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 230.516 241.641 1.04826
Squared ATP13A2 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] 32174 37487.2 1.16514
Rooted SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 59.6869 63.6262 1.066
780 Measured 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] 5874.76 6533.36 1.11211
Ranked POLR2F 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 TBP 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 PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] 62.2361 58.3858 1.06595
781 Measured SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490] 5874.76 6533.36 1.11211
Ranked MRTO4 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 TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 33900.6 39498 1.16511
Rooted 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] 62.2361 58.3858 1.06595
782 Measured 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] 5874.74 6533.33 1.11211
Ranked no value translin. [swissprot;acc:q15631] 224.385 235.131 1.04789
Squared KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 33893.6 39486.1 1.165
Rooted RPA2 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 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] 5874.78 6533.37 1.1121
Ranked TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] 224.385 235.131 1.04789
Squared no value hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 27407.7 31927.7 1.16492
Rooted PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 62.2361 58.3858 1.06595
784 Measured 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] 5874.77 6533.36 1.1121
Ranked PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] 224.385 235.131 1.04789
Squared no value dc11 protein. [refseq;acc:nm_020186] 27407.7 31927.7 1.16492
Rooted RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] 62.2361 58.3858 1.06595
785 Measured HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 4997 5557.17 1.1121
Ranked NET1 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 APPBP1 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905] 27407.7 31927.7 1.16492
Rooted CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 62.2332 58.3925 1.06577
786 Measured PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 9304.83 10347.3 1.11204
Ranked 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] 244.447 233.508 1.04685
Squared 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] 27407.7 31927.7 1.16492
Rooted RPS9 40s ribosomal protein s9. [swissprot;acc:p46781] 52.0101 48.813 1.0655
787 Measured ATP6V0A2 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 UTP20 down-regulated in metastasis. [refseq;acc:nm_014503] 244.447 233.508 1.04685
Squared UBE1C 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 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 64.5489 68.7769 1.0655
788 Measured TCIRG1 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 NFU1 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
- 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/