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 1051 to 1100 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
132 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Subtracted Low confidence 0 12716.5 10962.4 1754.1
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Divided 16411.9 14027.1 1.17001
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted High confidence 10883 12622.8 1739.8
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 19048 22389 1.1754
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted Low confidence 1 203.016 189.965 13.051
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Divided High confidence 350 290 1.2069
133 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] Low confidence 0 11236.1 13113.5 1.16709
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] High confidence 6814 8009 1.17537
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 1 226.887 194.72 32.167
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 17144.8 15405.6 1739.2
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 14922.7 13174.5 1748.2
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Divided 1 220.268 206.997 1.06411
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted 203.007 189.985 13.022
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided High confidence 350 290 1.2069
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 12314.9 10489.3 1.17404
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 290 1.2069
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 194.79 32.094
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Low confidence 0 16853 15123 1730
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 12157.6 13890.3 1732.7
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Divided Low confidence 9210.38 7893.05 1.1669
transgelin (smooth muscle protein 22-alpha) (sm22-alpha) (ws3-10) (22 kda actin-binding protein). [swissprot;acc:q01995] 1 218.561 205.431 1.06391
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Subtracted 218.36 205.4 12.96
135 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] High confidence 0 8871.11 10603.2 1732.09
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Divided 12314.9 10489.3 1.17404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 290 1.2069
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
neuronal protein np25. [swissprot;acc:q9ui15] Divided Low confidence 218.66 205.57 1.06368
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 0 15432.9 13250 1.16475
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 1 202.96 190.094 12.866
serpin b11. [swissprot;acc:q96p15] 0 16853 15123 1730
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided High confidence 12335.3 10506.8 1.17403
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Subtracted Low confidence 16853 15123 1730
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided High confidence 1 350 290 1.2069
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided Low confidence 202.996 190.854 1.06362
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted High confidence 0 12759.4 11028.8 1730.6
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Low confidence 1 219.344 206.52 12.824
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 0 12024.2 13977.2 1.16242
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] High confidence 12328.5 10501 1.17403
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted 1 263.191 231.394 31.797
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 0 19314 21041 1727
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Divided 11161.3 12965.5 1.16165
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Subtracted High confidence 16853 15123 1730
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 1 350 290 1.2069
testican-3 precursor. [swissprot;acc:q9bq16] Low confidence 220.395 234.389 1.0635
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 203.678 190.88 12.798
138 beta tubulin 1, class vi. [refseq;acc:nm_030773] 0 12794.3 14503.8 1709.5
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] High confidence 1 174.667 205.556 30.889
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Divided 0 12384.7 10549.4 1.17397
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Subtracted Low confidence 1 219.273 206.507 12.766

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/