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 [...,...].
description green Value Type Rank Interaction Map Gene Network Comparison Type red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
green
Rank
red
network_comparison
carboxypeptidase b precursor. [refseq;acc:nm_020361] 190.239 509 177.698 1.07057
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 211.685 717 223.121 1.05402
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 715
carcinoma related gene. [refseq;acc:nm_016041] 0.00001 3179 0.00001 1
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 214.69 1698 217.624 1.01367
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 0.00001 2885 0.00001 1
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 269.238 226 239.991 1.12187
casein kinase i alpha s-like. [refseq;acc:nm_145203] 225.237 1495 229.459 1.01874
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 1496
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 224.164 1721 227.125 1.01321
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 224.21 1710 227.225 1.01345
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 0.00001 2830 0.00001 1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 224.372 936 232.473 1.03611
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 230.957 863 240.194 1.03999
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 864
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 228.46 1292 233.942 1.024
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 182.459 1834 180.409 1.01136
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 211.898 1667 214.898 1.01416
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 219.157 1426 214.717 1.02068
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425
caveolin-1. [swissprot;acc:q03135] 0.00001 3099 0.00001 1
caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] 213.945 572 227.86 1.06504
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 203.237 762 213.256 1.0493
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 194.368 556 207.27 1.06638
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 204.309 36 260.532 1.27519
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 234.804 408 255.112 1.08649
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] 0.00001 3163 0.00001 1
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] 213.875 1390 218.47 1.02148
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] 0.00001 2958 0.00001 1
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 3226
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9] 2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 223.483 2075 221.703 1.00803
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 253.197 418 233.539 1.08417
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 420
cda11 protein. [refseq;acc:nm_032026] 209.732 1579 213.181 1.01644
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 214.286 1778 216.878 1.0121
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 226.459 437 209.921 1.07878
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 206.195 692 217.602 1.05532
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948] 0.00001 3209 0.00001 1
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 198.71 2155 200.063 1.00681
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 198.321 2739 198.278 1.00022
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 170.888 1585 168.145 1.01631
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 204.516 1481 208.432 1.01915
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 170.837 1583 168.091 1.01634
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 170.753 1581 168.002 1.01637
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535] 0.00001 2850 0.00001 1
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 2990

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/