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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description Hugo Rank Gene Value Type Network Comparison Type red Interaction Map Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Hugo
Rank
red
green
network_comparison
carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 509 177.698 190.239 1.07057
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] CPE 717 223.121 211.685 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] CPN1 715
carcinoma related gene. [refseq;acc:nm_016041] DERL2 3179 0.00001 0.00001 1
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] CRAT 1698 217.624 214.69 1.01367
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] CPT2 2885 0.00001 0.00001 1
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP 226 239.991 269.238 1.12187
casein kinase i alpha s-like. [refseq;acc:nm_145203] CSNK1A1L 1495 229.459 225.237 1.01874
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] CSNK1A1 1496
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] CSNK1D 1721 227.125 224.164 1.01321
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] no value 1710 227.225 224.21 1.01345
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] CSNK1G1 2830 0.00001 0.00001 1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] CSNK1G2 2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] CSNK1G3 2901
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] no value 936 232.473 224.372 1.03611
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] CSNK2A1P 863 240.194 230.957 1.03999
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] CSNK2A2 864
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] CASP7 1292 233.942 228.46 1.024
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] CTNNAL1 1834 180.409 182.459 1.01136
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] CTSB 1667 214.898 211.898 1.01416
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] CTSL1 1426 214.717 219.157 1.02068
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] CTSL2 1425
caveolin-1. [swissprot;acc:q03135] CAV1 3099 0.00001 0.00001 1
caveolin-3 (m-caveolin). [swissprot;acc:p56539] CAV3 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] no value 572 227.86 213.945 1.06504
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL 762 213.256 203.237 1.0493
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] CUTL1 556 207.27 194.368 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] NFYA 36 260.532 204.309 1.27519
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] CEBPZ 408 255.112 234.804 1.08649
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] CNOT3 3163 0.00001 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] CNOT4 1390 218.47 213.875 1.02148
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] CNOT6L 2958 0.00001 0.00001 1
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] no value 3226
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9] CNOT8 2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] CD109 2075 221.703 223.483 1.00803
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] CLEC4M 418 233.539 253.197 1.08417
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] CD209 420
cda11 protein. [refseq;acc:nm_032026] TATDN1 1579 213.181 209.732 1.01644
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] ARHGEF9 1778 216.878 214.286 1.0121
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] TRIP10 437 209.921 226.459 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] CDC5L 692 217.602 206.195 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] MNAT1 3209 0.00001 0.00001 1
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] CDIPT 2155 200.063 198.71 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] CHL1 2739 198.278 198.321 1.00022
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] CDC2 1585 168.145 170.888 1.01631
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] CDC23 1481 208.432 204.516 1.01915
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] CDK2 1583 168.091 170.837 1.01634
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] CDK3 1581 168.002 170.753 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] CDK5 2850 0.00001 0.00001 1
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] CDK8 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
- Hugo is the HGNC identifier if it exists
- 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/