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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 8262 to 8311 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2066 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Ranked 229.102 231.001 1.00829
ring finger protein 20. [refseq;acc:nm_019592] Rooted 59.5914 61.1533 1.02621
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Measured 5882.61 6213.34 1.05622
2067 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 3602.75 3411.18 1.05616
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Ranked 193.226 191.639 1.00828
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Rooted 66.6886 68.4366 1.02621
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Squared 24225.6 26399 1.08972
2068 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
fas apoptotic inhibitory molecule. [refseq;acc:nm_018147] Ranked 220.8 222.61 1.0082
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Measured 3602.75 3411.17 1.05616
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Rooted 59.5914 61.1533 1.02621
2069 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Measured 4632.65 4892.66 1.05613
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Ranked 217.555 215.807 1.0081
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Rooted 55.9946 57.4614 1.0262
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Squared 24225.6 26399 1.08972
2070 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
polybromo 1. [refseq;acc:nm_018165] Rooted 61.089 62.6862 1.02615
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Ranked 223.199 225.008 1.0081
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Measured 10178.5 9638.08 1.05607
2071 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 6437.24 6797.24 1.05592
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Squared 24225.6 26399 1.08972
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Ranked 217.555 215.807 1.0081
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Rooted 61.089 62.6862 1.02615
2072 dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Ranked 217.555 215.807 1.0081
enhancer of rudimentary homolog. [swissprot;acc:q14259] Measured 6437.24 6797.24 1.05592
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Squared 24225.6 26399 1.08972
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Rooted 61.089 62.6862 1.02615
2073 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Squared 24225.6 26399 1.08972
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Measured 6083.39 6423.12 1.05585
possible global transcription activator snf2l1. [swissprot;acc:p28370] Rooted 61.089 62.6862 1.02615
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Ranked 229.267 227.433 1.00806
2074 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Measured 3614.91 3423.89 1.05579
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Squared 34266.3 31445.7 1.0897
dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] Ranked 216.324 214.599 1.00804
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Rooted 61.089 62.6862 1.02615
2075 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Ranked 221.703 223.483 1.00803
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Rooted 61.089 62.6862 1.02615
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Measured 3614.91 3423.89 1.05579
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Squared 26521.6 28897.7 1.08959
2076 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] 25481.8 27764.1 1.08957
af-6 protein. [swissprot;acc:p55196] Measured 5746.65 6067.27 1.05579
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Ranked 221.703 223.483 1.00803
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Rooted 61.0883 62.6822 1.02609
2077 60s ribosomal protein l34. [swissprot;acc:p49207] Measured 3614.91 3423.89 1.05579
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] Squared 25481.8 27764.1 1.08957
dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Rooted 55.3465 53.9391 1.02609
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Ranked 221.703 223.483 1.00803
2078 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Squared 25481.8 27764.1 1.08957
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Rooted 62.3035 63.9253 1.02603
fidgetin-like 1. [refseq;acc:nm_022116] Ranked 215.511 213.814 1.00794

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/