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 25226 to 25275 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2652 nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Ranked Divided 201.451 201.673 1.0011
protein kinase nyd-sp25. [refseq;acc:nm_033516] Rooted Subtracted 66.5231 66.8631 0.34
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Ranked 194.097 194.328 0.231
tumor protein d52 (n8 protein). [swissprot;acc:p55327] Measured Divided 6349.55 6407.25 1.00909
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Subtracted 6349.23 6406.72 57.49
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Rooted Divided 70.0263 70.4067 1.00543
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Squared 17957.5 17466.2 1.02813
2653 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Rooted Subtracted 72.1844 72.5201 0.3357
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Ranked 194.097 194.328 0.231
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Squared 22249 22757.3 508.3
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] Rooted Divided 70.0263 70.4067 1.00543
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] Ranked 201.452 201.674 1.0011
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Measured Subtracted 3985.17 3928.38 56.79
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Divided 6349.23 6406.72 1.00905
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Squared 17924.8 17436.3 1.02802
2654 40s ribosomal protein s9. [swissprot;acc:p46781] Measured Subtracted 3933.74 3877.14 56.6
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134] Ranked 194.097 194.328 0.231
cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] Measured Divided 7118.22 7055.43 1.0089
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Squared Subtracted 22249 22757.3 508.3
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Ranked Divided 201.452 201.674 1.0011
protein kinase nyd-sp25. [refseq;acc:nm_033516] Rooted 66.5231 66.8631 1.00511
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Subtracted 72.1844 72.5201 0.3357
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Squared Divided 17923.2 17434.9 1.02801
2655 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Ranked 201.445 201.667 1.0011
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Rooted Subtracted 72.1844 72.5201 0.3357
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Divided 58.9993 59.2983 1.00507
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Measured 8290.91 8220.11 1.00861
nucleoporin like 1. [refseq;acc:nm_014089] Squared Subtracted 30868.3 31361.7 493.4
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Ranked 194.097 194.328 0.231
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Measured 5339.06 5395.25 56.19
zinc finger protein 232. [swissprot;acc:q9uny5] Squared Divided 17924 17435.6 1.02801
2656 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Rooted Subtracted 72.1844 72.5201 0.3357
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Ranked Divided 217.179 216.943 1.00109
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Rooted 58.9993 59.2983 1.00507
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Measured Subtracted 8222.61 8169.38 53.23
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Squared 30868.3 31361.7 493.4
thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755] Ranked 210.136 209.911 0.225
zinc finger protein 99. [refseq;acc:nm_032164] Squared Divided 17924.2 17435.8 1.02801
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Measured 4191.15 4226.86 1.00852
2657 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Rooted 58.9993 59.2983 1.00507
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Squared Subtracted 30868.3 31361.7 493.4
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] Ranked Divided 216.934 216.7 1.00108
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Measured Subtracted 4000.73 3947.54 53.19
lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754] Rooted 72.1844 72.5201 0.3357
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Ranked 201.37 201.594 0.224
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Measured Divided 5327.58 5371.47 1.00824
zinc finger protein 305. [swissprot;acc:o43309] Squared 17923.9 17435.6 1.02801
2658 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Rooted 58.9993 59.2983 1.00507
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Measured 8278.73 8211.05 1.00824
fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Squared Subtracted 36808.5 36316 492.5

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/