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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map red green network_comparison Filtered
Results: HTML CSV LaTeX Showing element 8241 to 8290 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1559 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Ranked 196.191 192.996 1.01655
eyes absent homolog 3. [swissprot;acc:q99504] Rooted 61.9436 64.1746 1.03602
tensin. [refseq;acc:nm_022648] Squared 27803.3 30910.9 1.11177
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Measured 6048.57 6487.65 1.07259
1560 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Squared 26174.3 29098.4 1.11172
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Rooted 66.302 68.6843 1.03593
p66 alpha. [refseq;acc:nm_017660] Ranked 167.687 170.455 1.01651
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Measured 6048.57 6487.65 1.07259
1561 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Squared 26174.3 29098.4 1.11172
mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257] Rooted 65.8508 68.2155 1.03591
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Ranked 167.687 170.455 1.01651
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Measured 6078.43 6519.6 1.07258
1562 26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805] Squared 26174.3 29098.4 1.11172
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Measured 5984.88 6419.11 1.07255
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Rooted 65.8508 68.2155 1.03591
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Ranked 167.687 170.455 1.01651
1563 apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114] Squared 26174.3 29098.4 1.11172
atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Ranked 218.277 214.739 1.01648
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Measured 6221.35 6672.51 1.07252
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Rooted 64.5089 66.8255 1.03591
1564 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Ranked 218.277 214.739 1.01648
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Squared 31878.5 35436.9 1.11162
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Measured 6257.62 6711.4 1.07252
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Rooted 65.8508 68.2155 1.03591
1565 eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Ranked 221.128 224.767 1.01646
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Squared 29530.9 32827.2 1.11162
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Measured 6343.76 6803.44 1.07246
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Rooted 64.5103 66.8259 1.0359
1566 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Ranked 221.128 224.767 1.01646
eyes absent homolog 1. [swissprot;acc:q99502] Rooted 61.9761 64.2003 1.03589
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Squared 2565.98 2308.67 1.11145
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Measured 5846.67 6269.41 1.0723
1567 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 5822.25 6242.94 1.07226
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Ranked 221.128 224.767 1.01646
megf11 protein. [refseq;acc:nm_032445] Squared 29503.9 32791.7 1.11144
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Rooted 61.97 64.1935 1.03588
1568 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Ranked 221.128 224.767 1.01646
megf10 protein. [refseq;acc:nm_032446] Squared 29503.5 32791.2 1.11143
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Measured 5845.22 6267.34 1.07222
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Rooted 61.9702 64.1936 1.03588
1569 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] 61.9705 64.1938
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Squared 29502.7 32790.1 1.11143
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Ranked 221.128 224.767 1.01646
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Measured 5819.37 6239.55 1.0722
1570 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Squared 26688.8 29658.6 1.11128
n-acetylglutamate synthase. [refseq;acc:nm_153006] Measured 5162.27 5534.71 1.07215
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Ranked 221.128 224.767 1.01646
ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Rooted 61.9703 64.1936 1.03588
1571 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] Measured 5851.64 6273.4 1.07208
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Ranked 221.128 224.767 1.01646

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/