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 green red network_comparison
Results: HTML CSV LaTeX Showing element 3080 to 3129 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1540 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 236.015 240.077 1.01721
1541 importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Subtracted 188.637 192.336 3.699
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Divided 218.92 222.672 1.01714
1542 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Subtracted 216.081 219.762 3.681
trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Divided 209.965 213.546 1.01706
1543 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
orphan nuclear receptor tr2. [swissprot;acc:p13056] Subtracted 216.083 219.76 3.677
1544 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] Divided 216.081 219.762 1.01704
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Subtracted 228.769 225.119 3.65
1545 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
orphan nuclear receptor tr2. [swissprot;acc:p13056] Divided 216.083 219.76 1.01702
1546 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] 221.474 217.769 1.01701
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Subtracted 228.769 225.119 3.65
1547 myb-related protein b (b-myb). [swissprot;acc:p10244] Divided 218.823 222.541 1.01699
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Subtracted 228.769 225.119 3.65
1548 eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] 224.767 221.128 3.639
myb-related protein a (a-myb). [swissprot;acc:p10243] Divided 218.802 222.512 1.01696
1549 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 221.424 225.159 1.01687
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Subtracted 224.767 221.128 3.639
1550 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided 221.424 225.159 1.01687
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Subtracted 224.767 221.128 3.639
1551 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Divided 221.424 225.159 1.01687
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 224.767 221.128 3.639
1552 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Divided 221.424 225.159 1.01687
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 224.767 221.128 3.639
1553 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Divided 211.833 215.389 1.01679
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Subtracted 224.767 221.128 3.639
1554 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Divided 193.018 196.215 1.01656
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Subtracted 224.767 221.128 3.639
1555 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Divided 192.996 196.192 1.01656
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Subtracted 224.767 221.128 3.639
1556 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Divided 192.996 196.192 1.01656
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Subtracted 227.219 223.589 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] 225.79 222.166 3.624
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 192.996 196.192 1.01656
1558 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 192.977 196.171 1.01655
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted 119.432 115.817 3.615
1559 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided 192.996 196.191 1.01655
tata element modulatory factor (tmf). [swissprot;acc:p82094] Subtracted 218.982 222.585 3.603
1560 p66 alpha. [refseq;acc:nm_017660] Divided 170.455 167.687 1.01651
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Subtracted 218.982 222.585 3.603
1561 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided 170.455 167.687 1.01651
1562 ammecr1 protein. [refseq;acc:nm_015365] Subtracted 218.982 222.585 3.603
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 170.455 167.687 1.01651
1563 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 214.739 218.277 1.01648
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Subtracted 218.982 222.585 3.603
1564 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 225.731 222.133 3.598
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Divided 214.739 218.277 1.01648
1565 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Subtracted 225.731 222.134 3.597

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/