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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6336 to 6385 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1584 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Rooted 61.9705 64.1938 1.03588
1585 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Measured 5858.48 6278.32 1.07166
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Ranked 168.145 170.888 1.01631
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Rooted 61.9703 64.1936 1.03588
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Squared 15537.9 17247.4 1.11002
1586 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] 26736.9 29677.3 1.10998
adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Ranked 222.166 225.79 1.01631
eyes absent homolog 4. [swissprot;acc:o95677] Rooted 61.9784 64.1991 1.03583
ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] Measured 5784.36 6198.73 1.07164
1587 parafibromin. [refseq;acc:nm_024529] Squared 17179.4 19067.8 1.10992
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Ranked 220.129 216.598 1.0163
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Rooted 64.7716 67.0877 1.03576
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Measured 5784.36 6198.73 1.07164
1588 pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Rooted 61.9974 64.2136 1.03575
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Squared 31589.1 35061.5 1.10992
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Ranked 177.834 180.725 1.01626
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Measured 3600.99 3360.33 1.07162
1589 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
eyes absent homolog 2. [swissprot;acc:o00167] Rooted 61.9889 64.2048 1.03575
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Squared 30900.2 34294.9 1.10986
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Ranked 223.589 227.219 1.01624
1590 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Squared 29261.2 32474.1 1.1098
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Measured 6364.01 6819.38 1.07155
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Rooted 62.7026 64.9366 1.03563
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Ranked 225.119 228.769 1.01621
1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Rooted 62.7026 64.9366 1.03563
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Measured 6364.01 6819.38 1.07155
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Squared 29261.2 32474.1 1.1098
1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Measured 5853.1 6271.79 1.07153
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Rooted 62.7026 64.9366 1.03563
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Squared 29261.2 32473.8 1.10979
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Ranked 225.119 228.769 1.01621
1593 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] Squared 29261.2 32473.8 1.10979
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Measured 4977.77 5333.78 1.07152
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Rooted 60.0929 62.2327 1.03561
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Ranked 225.119 228.769 1.01621
1594 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 222.133 225.731 1.0162
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Squared 29261.2 32473.8 1.10979
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Rooted 64.5338 66.8288 1.03556
transportin-sr; importin 12. [refseq;acc:nm_012470] Measured 5184.94 5555.76 1.07152
1595 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Ranked 222.134 225.731 1.01619
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Rooted 55.3706 57.3394 1.03556
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Measured 6351.32 6805.39 1.07149
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Squared 17195.6 19080.9 1.10964
1596 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Ranked 222.134 225.731 1.01619
enigma protein; lim domain protein. [refseq;acc:nm_005451] Measured 5665.34 6070.32 1.07148
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Rooted 55.3706 57.3394 1.03556
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Squared 25787.8 28614.7 1.10962
1597 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Ranked 222.134 225.731 1.01619

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/