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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 red green network_comparison
Results: HTML CSV LaTeX Showing element 9586 to 9635 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1199 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Squared Subtracted 22572.2 25647.6 3075.4
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Rooted 59.9298 62.8125 2.8827
n-myc proto-oncogene protein. [swissprot;acc:p04198] Squared Divided 20816.6 23663.1 1.13674
peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68] Measured Subtracted 5489.99 5986.63 496.64
pxr2b protein. [refseq;acc:nm_016559] Rooted Divided 66.7327 69.832 1.04644
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Measured 5449.48 5921.77 1.08667
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Ranked 241.496 235.508 1.02543
1200 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Squared Subtracted 26696.5 29768.6 3072.1
glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Divided 26914.1 30594.2 1.13674
homeobox protein otx1. [swissprot;acc:p32242] Rooted 56.0736 58.677 1.04643
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Ranked Subtracted 219.354 224.699 5.345
phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Measured 5489.99 5986.63 496.64
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Ranked Divided 219.03 213.604 1.0254
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Measured 5950.27 6465.72 1.08663
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Rooted Subtracted 61.4869 64.3691 2.8822
1201 cone-rod homeobox protein. [swissprot;acc:o43186] Divided 56.0896 58.6931 1.04642
keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Ranked Subtracted 219.354 224.699 5.345
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Squared 26696.5 29768.6 3072.1
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Divided 19317.7 21958.6 1.13671
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Rooted Subtracted 68.9332 71.8139 2.8807
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Measured 6523.17 7019.44 496.27
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Ranked Divided 210.986 216.344 1.0254
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Measured 6042.31 6565.03 1.08651
1202 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Squared Subtracted 26696.5 29768.6 3072.1
diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] Ranked Divided 227.274 233.041 1.02537
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Rooted Subtracted 68.9332 71.8139 2.8807
kappa b-ras 1. [refseq;acc:nm_020345] Measured 5721.19 6217.2 496.01
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Ranked 219.354 224.699 5.345
myb-related protein b (b-myb). [swissprot;acc:p10244] Rooted Divided 60.1108 62.9002 1.0464
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Measured 4913.07 5337.95 1.08648
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Squared 19317.7 21958.6 1.13671
1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Measured 4322.65 4696.04 1.08638
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Subtracted 5721.19 6217.2 496.01
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Ranked 219.354 224.699 5.345
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Squared 26696.5 29768.6 3072.1
myb-related protein a (a-myb). [swissprot;acc:p10243] Rooted Divided 60.1161 62.9033 1.04636
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Subtracted 68.9332 71.8139 2.8807
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Ranked Divided 219.023 213.606 1.02536
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Squared 19317.7 21958.6 1.13671
1204 keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked Subtracted 219.354 224.699 5.345
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Divided 219.022 213.607 1.02535
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Rooted 63.2865 66.2117 1.04622
snare associated protein snapin. [refseq;acc:nm_012437] Measured Subtracted 5721.19 6217.2 496.01
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Divided 5946.33 6459.79 1.08635
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Rooted Subtracted 68.9332 71.8139 2.8807
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Squared Divided 19317.7 21958.6 1.13671
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Subtracted 27757.7 30828.3 3070.6
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Measured Divided 5946.33 6459.79 1.08635
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Ranked Subtracted 219.354 224.699 5.345
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Squared 20465.9 23535.3 3069.4

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/