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 1244 to 1293 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
156 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Subtracted 9035 7279.6 1755.4
nuclear protein ukp68. [refseq;acc:nm_024824] Ranked 227.491 199.458 28.033
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Divided 249.663 298.263 1.19466
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 1.40528
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Rooted 56.3447 66.124 1.17356
157 brain protein 44. [swissprot;acc:o95563] Squared 89182.8 125229 1.40418
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 1.17351
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 23693.7 18263 1.29736
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared Subtracted 76438 58889.7 17548.3
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted 55.1113 67.5537 12.4424
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 7279.6 1755.4
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked 312 284 28
transcription factor lbx1. [swissprot;acc:p52954] Divided 249.663 298.263 1.19466
158 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted 56.3507 66.1252 1.17346
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked Subtracted 312 284 28
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Squared 76360.8 58841.7 17519.1
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured Divided 23693.7 18263 1.29736
mosaic protein lgn. [swissprot;acc:p81274] Ranked 249.663 298.263 1.19466
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Measured Subtracted 9035 7279.6 1755.4
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Rooted 149.397 136.972 12.425
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared Divided 89182.8 125229 1.40418
159 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked Subtracted 312 284 28
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared 76296.4 58801.6 17494.8
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 9035 7279.6 1755.4
necdin. [swissprot;acc:q99608] Divided 23693.7 18263 1.29736
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Ranked 249.663 298.263 1.19466
rna-binding protein. [refseq;acc:nm_019027] Rooted 52.7642 61.9019 1.17318
septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 1.40359
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted Subtracted 113.983 101.979 12.004
160 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Divided 52.7642 61.9019 1.17318
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Measured Subtracted 9035 7279.6 1755.4
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked Divided 249.663 298.263 1.19466
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 1.40126
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted Subtracted 43.4291 31.7159 11.7132
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured Divided 23693.7 18263 1.29736
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked Subtracted 312 284 28
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Squared 42788.3 60162.6 17374.3
161 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 173408 242989 1.40126
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Subtracted 9035 7279.6 1755.4
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked 312 284 28
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted Divided 52.7642 61.9019 1.17318
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted 43.4519 31.7522 11.6997
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked Divided 249.663 298.263 1.19466
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Squared Subtracted 52591.3 69845.1 17253.8
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 142 170 28
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted Divided 52.7642 61.9019 1.17318
high-mobility group 20a. [refseq;acc:nm_018200] Measured Subtracted 5140.14 6893.53 1753.39
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared Divided 173408 242989 1.40126
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Rooted Subtracted 43.4554 31.7576 11.6978

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/