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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Gene description Rank Value Type Filtered Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 601 to 650 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
network_comparison
green
red
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 1496 1 1.01874 225.237 229.459
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1721 1.01321 224.164 227.125
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 1.01345 224.21 227.225
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 1 0.00001 0.00001
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] 936 1.03611 224.372 232.473
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 863 1.03999 230.957 240.194
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] 1292 1.024 228.46 233.942
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 1834 1.01136 182.459 180.409
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 1667 1.01416 211.898 214.898
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 1426 1.02068 219.157 214.717
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425
caveolin-1. [swissprot;acc:q03135] 3099 1 0.00001 0.00001
caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] 572 1.06504 213.945 227.86
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 762 1.0493 203.237 213.256
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 556 1.06638 194.368 207.27
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] 36 1.27519 204.309 260.532
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 408 1.08649 234.804 255.112
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] 3163 1 0.00001 0.00001
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] 1390 1.02148 213.875 218.47
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] 2958 1 0.00001 0.00001
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 160 0 1.15331 13530.6 11732
3226 1 1 0.00001 0.00001
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9] 2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 2075 1.00803 223.483 221.703
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 418 1.08417 253.197 233.539
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 420
cda11 protein. [refseq;acc:nm_032026] 1579 1.01644 209.732 213.181
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 1778 1.0121 214.286 216.878
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 437 1.07878 226.459 209.921
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] 692 1.05532 206.195 217.602
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] 3209 1 0.00001 0.00001
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 2155 1.00681 198.71 200.063
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] 451 0 1.01987 13737.2 14010.2
2739 1 1.00022 198.321 198.278
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 1585 1.01631 170.888 168.145
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 1481 1.01915 204.516 208.432
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 1583 1.01634 170.837 168.091
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 245 0 1.09702 13019 11867.6
1581 1 1.01637 170.753 168.002
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] 2850 1 0.00001 0.00001
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 38 0 1.48976 10771 7230
2990 1 1 0.00001 0.00001
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] 2974
cellular modulator of immune recognition. [refseq;acc:nm_145021] 1179 1.02593 212.672 218.186
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 699 1.05413 209.118 220.438
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 705

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/