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 201 to 250 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
26 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Squared 0 44.3683 0.344399 128.828
Rooted 13.7805 3.80565 3.62106
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Ranked 12128.3 7533.33 1.60995
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Measured 153 662 4.3268
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Rooted 1 40.3362 24.2954 1.66024
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Measured 1833.01 892.67 2.0534
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Squared 143.692 457.521 3.18404
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Ranked 58 44 1.31818
27 dystrophin. [swissprot;acc:p11532] Rooted 0 17.8026 5.12693 3.47237
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured 1 1834.33 895.134 2.04922
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Rooted 40.3364 24.2968 1.66015
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Ranked 58 44 1.31818
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Squared 143.692 457.521 3.18404
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Measured 0 570 139 4.10072
ptd016 protein. [refseq;acc:nm_016125] Ranked 18050 11234 1.60673
syntaxin 10 (syn10). [swissprot;acc:o60499] Squared 4.29982 0.109658 39.2112
28 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Measured 570 139 4.10072
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked 1 201.949 153.671 1.31416
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Rooted 40.3372 24.3043 1.65967
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured 1834.36 895.194 2.04912
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Squared 143.692 457.521 3.18404
p28 ing5. [refseq;acc:nm_032329] Ranked 0 12124.8 7562.05 1.60337
ptd016 protein. [refseq;acc:nm_016125] Squared 0.213018 5.90864 27.7377
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 9.62443 3.64637 2.63946
29 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Squared 1 143.692 457.521 3.18404
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured 1834.52 895.507 2.04858
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Rooted 0 17.7955 7.34614 2.42243
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Ranked 7395 11625 1.57201
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 111.278 434.911 3.90833
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Squared 5.18438 141.427 27.2794
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Rooted 1 26.0288 43.1914 1.65937
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Ranked 187.458 243.678 1.29991
30 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] 0 7395 11625 1.57201
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Squared 1 143.692 457.521 3.18404
dystrophin. [swissprot;acc:p11532] Measured 0 427.217 111.739 3.82335
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 1 1834.59 895.633 2.04837
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Rooted 26.0288 43.1914 1.65937
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Squared 0 6.25494 141.944 22.6931
ptd016 protein. [refseq;acc:nm_016125] Rooted 5.47723 12.5698 2.29492
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Ranked 1 187.457 243.678 1.29991
31 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Squared 9924.76 25146.6 2.53372
dok-like protein. [refseq;acc:nm_024872] Measured 0 35 0.00001 3500000
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Squared 5.54059 103.726 18.7211
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured 1 1834.63 895.697 2.04827
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Ranked 0 8082.33 5266.67 1.53462
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Rooted 12.1655 27.8029 2.28539
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] 1 26.0288 43.1914 1.65937
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Ranked 187.458 243.677 1.2999
32 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 25146.6 2.53372
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] Measured 0 598 184 3.25

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/