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 Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Rank
description
Interaction Map
red
Filtered
green
network_comparison
26 cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] Low confidence 286.347 1 238.454 1.20085
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] High confidence 12128.3 0 7533.33 1.60995
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Low confidence 9282.29 6526.57 1.42223
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] High confidence 58 1 44 1.31818
27 camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211] Low confidence 13109 0 18516 1.41246
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 284.798 1 237.743 1.19792
mitochondrial solute carrier protein. [refseq;acc:nm_145305] High confidence 58 44 1.31818
ptd016 protein. [refseq;acc:nm_016125] 18050 0 11234 1.60673
28 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Low confidence 142 1 170 1.19718
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 201.949 153.671 1.31416
elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] Low confidence 16116.4 0 11505 1.40082
p28 ing5. [refseq;acc:nm_032329] High confidence 12124.8 7562.05 1.60337
29 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Low confidence 203.115 1 170.557 1.19089
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] High confidence 7395 0 11625 1.57201
solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246] Low confidence 12129.6 8687.07 1.39628
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 187.458 1 243.678 1.29991
30 alpha 2 globin. [refseq;acc:nm_000517] Low confidence 11486.2 0 15987.1 1.39185
bcl2-related ovarian killer. [refseq;acc:nm_032515] 265.638 1 223.235 1.18995
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] High confidence 7395 0 11625 1.57201
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 187.457 1 243.678 1.29991
31 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Low confidence 57.395 48.8186 1.17568
hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] 11485.6 0 15984.3 1.39168
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] High confidence 8082.33 5266.67 1.53462
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 187.458 1 243.677 1.2999
32 importin 9. [refseq;acc:nm_018085] 13292.2 0 8691.76 1.52929
myoglobin. [swissprot;acc:p02144] Low confidence 11485.4 15983.3 1.39162
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 273.188 1 232.49 1.17505
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] High confidence 187.462 243.673 1.29985
33 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Low confidence 210.241 246.125 1.17068
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] 20324.1 0 14746.1 1.37827
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] High confidence 13292.2 8691.76 1.52929
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 188.688 1 242.742 1.28647
34 fibrillin 3. [refseq;acc:nm_032447] Low confidence 5450.5 0 7506.66 1.37724
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] High confidence 11284 17173.8 1.52196
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence 155.56 1 133.876 1.16197
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] High confidence 189.07 242.453 1.28235
35 nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 3208.8 0 4871.6 1.5182
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 260.532 1 204.309 1.27519
protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] Low confidence 11808.5 0 16243 1.37553
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 297.273 1 258.59 1.14959
36 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] High confidence 260.532 204.309 1.27519
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 22422 0 14964 1.4984
sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 13052.7 9520.8 1.37097
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 296.837 1 258.33 1.14906
37 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 250.244 217.843 1.14874
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] High confidence 3859 0 2582 1.49458
myotubularin related protein 8. [refseq;acc:nm_017677] Low confidence 12302 8993.6 1.36786
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] High confidence 322 1 253 1.27273
38 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 7230 0 10771 1.48976
glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] Low confidence 247.202 1 282.937 1.14456

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/