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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 12214 to 12263 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
1527 PSMC3 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] Measured Divided 5926.76 6362.33 1.07349
STARD3NL mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Ranked 219.306 223.179 1.01766
UTP14A serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Rooted 64.0491 66.3884 1.03652
1528 ANK3 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Measured Subtracted 5916.05 6350.53 434.48
CAMK2G calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Rooted Divided 63.304 65.6156 1.03652
ERBB3 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Subtracted 60.3015 62.6331 2.3316
EXOSC4 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Squared 17541.4 20148.6 2607.2
FOXA3 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Ranked Divided 217.785 214.021 1.01759
HAL histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Squared 28606.2 31850.3 1.11341
MLLT4 af-6 protein. [swissprot;acc:p55196] Ranked Subtracted 218.733 214.98 3.753
TENC1 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Measured Divided 5869.97 6301.24 1.07347
1529 ACTG1 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Ranked 216.762 213.031 1.01751
ANK2 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Measured Subtracted 5916.05 6350.53 434.48
CAMK2D calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] Rooted Divided 63.304 65.6156 1.03652
DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Measured 5916.05 6350.53 1.07344
EGFR epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Rooted Subtracted 60.3015 62.6328 2.3313
EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Squared 17541.4 20148.6 2607.2
MYB myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Ranked 222.672 218.92 3.752
RPS6KA6 ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Squared Divided 28606.2 31850.3 1.11341
1530 ADAMTS9 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Measured 5916.05 6350.53 1.07344
ARL3 adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Subtracted 434.48
CDC25B m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Ranked 260.269 256.531 3.738
ERBB2 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] Rooted 60.3015 62.6328 2.3313
EXOSC3 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Squared 17541.4 20148.6 2607.2
MAP3K6 mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Rooted Divided 63.304 65.6156 1.03652
MLLT4 af-6 protein. [swissprot;acc:p55196] Ranked 218.733 214.98 1.01746
RPS6KA2 ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] Squared 28606.2 31850.3 1.11341
1531 no value signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Rooted 63.3039 65.6156 1.03652
CAMK2A calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] Squared 28606.2 31850.3 1.11341
CRIM1 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Ranked 217.025 213.304 1.01744
DCTN2 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Subtracted 225.159 221.424 3.735
DFFA dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Measured Divided 5916.05 6350.53 1.07344
EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Squared Subtracted 17541.4 20148.6 2607.2
UNC119 unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Measured 5916.05 6350.53 434.48
VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Rooted 63.2569 65.5867 2.3298
1532 ANK3 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Measured Divided 5916.05 6350.53 1.07344
CAMK2B calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] Squared 28606.2 31850.3 1.11341
MRPS16 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Subtracted 21512.7 24115.7 2603
PSMD8 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] Measured 5916.05 6350.53 434.48
RBM10 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Ranked Divided 228.419 232.376 1.01732
RPS6KA1 ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Rooted 63.304 65.6156 1.03652
SLC25A6 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Ranked Subtracted 225.159 221.424 3.735
VPS11 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Rooted 63.2569 65.5867 2.3298
1533 no value mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Squared Divided 28606.2 31850.3 1.11341
ABCD3 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Rooted 63.304 65.6156 1.03652
ANK2 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Measured 5916.05 6350.53 1.07344
CYCS cytochrome c. [swissprot;acc:p00001] Ranked 228.419 232.376 1.01732
FIGNL1 fidgetin-like 1. [refseq;acc:nm_022116] Squared Subtracted 28497.2 31100 2602.8
SLC25A4 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Ranked 225.159 221.424 3.735
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Measured 4713.58 4279.17 434.41

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/