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 12314 to 12363 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2577 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Ranked 192.625 192.922 1.00154
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Rooted 71.5023 72.1247 1.0087
translin. [swissprot;acc:q15631] Measured 4979.44 5071.53 1.01849
2578 40s ribosomal protein s26. [swissprot;acc:p02383] Squared 23172.9 22157.6 1.04582
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Ranked 213.422 213.75 1.00154
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Rooted 71.5023 72.1247 1.0087
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Measured 4979.44 5071.53 1.01849
2579 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Squared 23172.9 22157.6 1.04582
nitrilase 1. [refseq;acc:nm_005600] Ranked 213.422 213.75 1.00154
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Measured 4979.44 5071.53 1.01849
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Rooted 71.504 72.1264 1.0087
2580 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Squared 23172.9 22157.6 1.04582
disrupter of silencing 10. [refseq;acc:nm_020368] Rooted 71.5023 72.1247 1.0087
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Measured 4331.39 4252.8 1.01848
utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939] Ranked 213.422 213.75 1.00154
2581 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Measured 4570.81 4654.97 1.01841
dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941] Ranked 213.428 213.756 1.00154
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Squared 23172.9 22157.6 1.04582
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Rooted 71.5025 72.1249 1.0087
2582 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Squared 23107 22137 1.04382
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Measured 3899.28 3829.53 1.01821
lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182] Ranked 213.422 213.75 1.00154
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Rooted 71.5034 72.1258 1.0087
2583 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 59.5216 60.0368 1.00866
dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8] Ranked 213.415 213.743 1.00154
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Measured 3926.4 3857.88 1.01776
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Squared 31221.5 32578.2 1.04345
2584 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Measured 4180.32 4253.46 1.0175
dystrophin. [swissprot;acc:p11532] Ranked 213.422 213.75 1.00154
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Squared 36431.8 34958.8 1.04214
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Rooted 59.5213 60.0364 1.00865
2585 angiomotin. [refseq;acc:nm_133265] Ranked 213.422 213.75 1.00154
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Rooted 59.5205 60.0353 1.00865
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Squared 28228.7 29412.6 1.04194
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Measured 4180.32 4253.46 1.0175
2586 angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201] Ranked 213.422 213.75 1.00154
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Measured 4180.32 4253.46 1.0175
tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Rooted 59.5189 60.0331 1.00864
wd repeat domain 26. [refseq;acc:nm_025160] Squared 32575.7 33907 1.04087
2587 alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424] Ranked 213.422 213.75 1.00154
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Rooted 55.9762 55.5001 1.00858
insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] Squared 36688.8 35252 1.04076
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Measured 4180.32 4253.46 1.0175
2588 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] Ranked 222.305 222.64 1.00151
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Rooted 45.2905 44.9065 1.00855
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Measured 4180.32 4253.46 1.0175
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Squared 34721.5 36133.4 1.04066
2589 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Measured 7181.3 7057.99 1.01747
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Ranked 212.74 212.422 1.0015
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Rooted 62.9549 63.4703 1.00819

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/