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 12414 to 12463 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1552 lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Ranked Subtracted 221.128 224.767 3.639
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Rooted Divided 63.8754 66.1935 1.03629
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Squared 27018.7 30041.5 1.11188
1553 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Ranked 215.389 211.833 1.01679
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Rooted 54.3745 52.4728 1.03624
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] Squared 27018.7 30041.5 1.11188
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Subtracted 25629.5 28203.8 2574.3
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Rooted 63.304 65.6156 2.3116
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked 221.128 224.767 3.639
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Measured Divided 5875.75 6302.76 1.07267
tensin. [refseq;acc:nm_022648] Subtracted 5871.89 6303.56 431.67
1554 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Squared Divided 26642.1 29622.1 1.11185
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Measured Subtracted 6830.4 7261.98 431.58
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Rooted Divided 63.9658 66.2831 1.03623
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Ranked 196.215 193.018 1.01656
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Subtracted 221.128 224.767 3.639
prefoldin subunit 1. [swissprot;acc:o60925] Measured Divided 5875.75 6302.76 1.07267
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Rooted Subtracted 63.304 65.6156 2.3116
shc transforming protein. [swissprot;acc:p29353] Squared 25629.5 28203.8 2574.3
1555 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Rooted 63.304 65.6156 2.3116
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Ranked Divided 196.192 192.996 1.01656
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Subtracted 221.128 224.767 3.639
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Measured Divided 5875.75 6302.76 1.07267
target of myb protein 1. [swissprot;acc:o60784] Squared 24710 27473.8 1.11185
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Rooted 63.4077 65.7034 1.03621
zasp protein (fragment). [sptrembl;acc:q9y4z3] Measured Subtracted 5671.93 6103.49 431.56
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Squared 25629.5 28203.8 2574.3
1556 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Ranked Divided 196.192 192.996 1.01656
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Measured Subtracted 5869.97 6301.24 431.27
choline dehydrogenase. [refseq;acc:nm_018397] Divided 5875.75 6302.76 1.07267
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Rooted Subtracted 63.304 65.6156 2.3116
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Squared Divided 24712.8 27476.2 1.11182
kccr13l. [refseq;acc:nm_139179] Rooted 61.0148 63.2233 1.0362
neuronal shc. [refseq;acc:nm_016848] Squared Subtracted 25629.5 28203.8 2574.3
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Ranked 223.589 227.219 3.63
1557 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 222.166 225.79 3.624
adp-ribosylation factor 1. [swissprot;acc:p32889] Squared 25629.5 28203.8 2574.3
dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Rooted Divided 61.0148 63.2233 1.0362
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Subtracted 63.304 65.6156 2.3116
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Measured 4062.03 4492.48 430.45
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Squared Divided 24712.9 27476.3 1.11182
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Measured 6018.7 6455.7 1.07261
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Ranked 196.192 192.996 1.01656
1558 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 196.171 192.977 1.01655
calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] Rooted Subtracted 63.304 65.6156 2.3116
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Ranked 115.817 119.432 3.615
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Squared 25629.5 28203.8 2574.3
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Rooted Divided 61.6942 63.9187 1.03606
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Squared 24716.5 27479.3 1.11178
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Measured Subtracted 5870.72 6300.83 430.11

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/