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 3080 to 3129 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1540 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 2 (ec 2.6.1.16) (hexosephosphate aminotransferase 2) (d-fructose-6- phosphate amidotransferase 2) (gfat 2) (gfat2). [swissprot;acc:o94808] Low confidence 201.26 197.072 1.02125
1541 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 203.321 199.093 1.02124
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] High confidence 222.672 218.92 1.01714
1542 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] 213.546 209.965 1.01706
vav-2 protein. [swissprot;acc:p52735] Low confidence 200.389 196.224 1.02123
1543 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] High confidence 213.546 209.965 1.01706
homeobox protein hox-b6 (hox-2b) (hox-2.2) (hu-2). [swissprot;acc:p17509] Low confidence 203.129 198.906 1.02123
1544 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] High confidence 219.762 216.081 1.01704
park2 co-regulated; parkin co-regulated gene protein. [refseq;acc:nm_152410] Low confidence 203.124 198.907 1.0212
1545 orphan nuclear receptor tr2. [swissprot;acc:p13056] High confidence 219.76 216.083 1.01702
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Low confidence 199.511 195.372 1.02119
1546 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] High confidence 217.769 221.474 1.01701
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Low confidence 201.261 197.087 1.02118
1547 myb-related protein b (b-myb). [swissprot;acc:p10244] High confidence 222.541 218.823 1.01699
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Low confidence 202.348 198.152 1.02118
1548 myb-related protein a (a-myb). [swissprot;acc:p10243] High confidence 222.512 218.802 1.01696
ubiquitin conjugation factor e4 b (ubiquitin-fusion degradation protein 2) (homozygously deleted in neuroblastoma-1). [swissprot;acc:o95155] Low confidence 202.493 198.294 1.02118
1549 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] 205.847 201.577
dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] High confidence 225.159 221.424 1.01687
1550 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
ras-related protein rab-6c (rab6-like protein wth3). [swissprot;acc:q9h0n0] Low confidence 200.571 196.413 1.02117
1551 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] High confidence 225.159 221.424 1.01687
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Low confidence 201.491 197.313 1.02117
1552 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] High confidence 225.159 221.424 1.01687
homeobox protein hox-a6 (hox-1b). [swissprot;acc:p31267] Low confidence 203.119 198.908 1.02117
1553 adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] High confidence 215.389 211.833 1.01679
adrenoleukodystrophy protein (aldp). [swissprot;acc:p33897] Low confidence 202.418 206.704 1.02117
1554 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] High confidence 196.215 193.018 1.01656
ras-related protein rab-6b. [swissprot;acc:q9nrw1] Low confidence 200.567 196.41 1.02116
1555 pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] High confidence 196.192 192.996 1.01656
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Low confidence 202.345 198.152 1.02116
1556 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] High confidence 196.192 192.996 1.01656
selenoprotein t. [swissprot;acc:q9nzj3] Low confidence 205.836 201.572 1.02115
1557 l-threonine dehydrogenase; l-threonine 3-dehydrogenase. [refseq;acc:nm_152566]
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 196.192 192.996 1.01656
1558 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 196.171 192.977 1.01655
ras-related protein rab-6a (rab-6). [swissprot;acc:p20340] Low confidence 200.545 196.394 1.02114
1559 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] High confidence 196.191 192.996 1.01655
nucleolar cysteine-rich protein; zinc finger autoantigen 330. [refseq;acc:nm_014487] Low confidence 205.98 201.716 1.02114
1560 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] 197.747 193.656 1.02113
p66 alpha. [refseq;acc:nm_017660] High confidence 167.687 170.455 1.01651
1561 nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [swissprot;acc:o14595] Low confidence 201.534 197.366 1.02112
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] High confidence 167.687 170.455 1.01651
1562 nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Low confidence 199.989 195.852 1.02112
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] High confidence 167.687 170.455 1.01651
1563 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 218.277 214.739 1.01648
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Low confidence 197.752 193.661 1.02112
1564 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] High confidence 218.277 214.739 1.01648
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Low confidence 197.74 193.65 1.02112
1565 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] 199.975 195.839

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/