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 3101 to 3150 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1551 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] Divided 5732.83 6149.86 1.07274
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Subtracted 5672.24 6103.99 431.75
1552 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Divided 6025.86 6464.16 1.07274
collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Subtracted 5672.2 6103.92 431.72
1553 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Divided 5875.75 6302.76 1.07267
tensin. [refseq;acc:nm_022648] Subtracted 5871.89 6303.56 431.67
1554 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 6830.4 7261.98 431.58
prefoldin subunit 1. [swissprot;acc:o60925] Divided 5875.75 6302.76 1.07267
1555 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
zasp protein (fragment). [sptrembl;acc:q9y4z3] Subtracted 5671.93 6103.49 431.56
1556 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] 5869.97 6301.24 431.27
choline dehydrogenase. [refseq;acc:nm_018397] Divided 5875.75 6302.76 1.07267
1557 t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 4062.03 4492.48 430.45
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 6018.7 6455.7 1.07261
1558 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Subtracted 5870.72 6300.83 430.11
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Divided 6048.57 6487.65 1.07259
1559 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Subtracted 4063.64 4492.98 429.34
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Divided 6048.57 6487.65 1.07259
1560 pbk1 protein. [sptrembl;acc:o76021] Subtracted 4064.23 4493.36 429.13
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Divided 6048.57 6487.65 1.07259
1561 dpy-30-like protein. [swissprot;acc:q9c005] Subtracted 5602.01 6031.05 429.04
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Divided 6078.43 6519.6 1.07258
1562 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 5984.88 6419.11 1.07255
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Subtracted 5602.01 6031.05 429.04
1563 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
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] Divided 6221.35 6672.51 1.07252
1564 neighbor of cox4. [swissprot;acc:o43402] Subtracted 5602.01 6031.05 429.04
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] Divided 6257.62 6711.4 1.07252
1565 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] 6343.76 6803.44 1.07246
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Subtracted 5602.01 6031.05 429.04
1566 potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Divided 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
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Subtracted 6035.6 6464.5 428.9
1568 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Divided 5845.22 6267.34 1.07222
1569 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] Subtracted 6035.6 6464.5 428.9
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Divided 5819.37 6239.55 1.0722
1570 mitochondrial precursor proteins import receptor (translocase of outer membrane tom70). [swissprot;acc:o94826] Subtracted 6035.6 6464.5 428.9
n-acetylglutamate synthase. [refseq;acc:nm_153006] Divided 5162.27 5534.71 1.07215
1571 26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665] 5851.64 6273.4 1.07208
lim homeobox transcription factor 1 beta (lim/homeobox protein lmx1b) (lim-homeobox protein 1.2) (lmx-1.2). [swissprot;acc:o60663] Subtracted 6035.6 6464.5 428.9
1572 proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Divided 6068.03 6504.59 1.07194
proteasome subunit beta type 2 (ec 3.4.25.1) (proteasome component c7-i) (macropain subunit c7-i) (multicatalytic endopeptidase complex subunit c7-i). [swissprot;acc:p49721] Subtracted 6035.6 6464.5 428.9
1573 adp-ribosylation factor-like protein 1. [swissprot;acc:p40616]
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Divided 11785.4 10995.3 1.07186
1574 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 5106.13 5472.96 1.07184
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Subtracted 6858.84 7287.27 428.43
1575 dc11 protein. [refseq;acc:nm_020186]
dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Divided 5106.13 5472.96 1.07184

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/