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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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 description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 8241 to 8290 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
green
red
network_comparison
2061 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] Measured 5865.84 5552.69 1.0564
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Squared 26399 24225.6 1.08972
dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989] Rooted 68.5831 66.825 1.02631
tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] Ranked 216.981 218.79 1.00834
2062 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Measured 5865.85 5552.7 1.0564
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Rooted 68.5831 66.825 1.02631
tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Ranked 216.981 218.79 1.00834
zinc finger protein 258. [refseq;acc:nm_145310] Squared 26399 24225.6 1.08972
2063 cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4] Rooted 66.9218 65.2079 1.02628
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Ranked 205.923 207.638 1.00833
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] Measured 5952.14 5634.63 1.05635
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] Squared 26399 24225.6 1.08972
2064 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Rooted 63.8594 62.2279 1.02622
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] Measured 5861.31 5548.79 1.05632
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Ranked 205.939 207.655 1.00833
zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095] Squared 26399 24225.6 1.08972
2065 60s ribosomal protein l35. [swissprot;acc:p42766] Measured 3410.23 3602.25 1.05631
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142] Squared 26399 24225.6 1.08972
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] Rooted 62.6908 61.0898 1.02621
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Ranked 212.561 214.328 1.00831
2066 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Squared 26399 24225.6 1.08972
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Ranked 231.001 229.102 1.00829
ring finger protein 20. [refseq;acc:nm_019592] Rooted 61.1533 59.5914 1.02621
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Measured 6213.34 5882.61 1.05622
2067 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 3411.18 3602.75 1.05616
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Ranked 191.639 193.226 1.00828
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Rooted 68.4366 66.6886 1.02621
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Squared 26399 24225.6 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 222.61 220.8 1.0082
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Measured 3411.17 3602.75 1.05616
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Rooted 61.1533 59.5914 1.02621
2069 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Measured 4892.66 4632.65 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 215.807 217.555 1.0081
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] Rooted 57.4614 55.9946 1.0262
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Squared 26399 24225.6 1.08972
2070 actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
polybromo 1. [refseq;acc:nm_018165] Rooted 62.6862 61.089 1.02615
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Ranked 225.008 223.199 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 9638.08 10178.5 1.05607
2071 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 6797.24 6437.24 1.05592
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Squared 26399 24225.6 1.08972
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Ranked 215.807 217.555 1.0081
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Rooted 62.6862 61.089 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 215.807 217.555 1.0081
enhancer of rudimentary homolog. [swissprot;acc:q14259] Measured 6797.24 6437.24 1.05592
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Squared 26399 24225.6 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 62.6862 61.089 1.02615
2073 actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Squared 26399 24225.6 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 6423.12 6083.39 1.05585

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/