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 Value Type Rank Interaction Map description Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
101 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided 1 2353.63 3225.65 1.3705
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 0 638.862 330.189 308.673
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Divided 1442 977 1.47595
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Subtracted 1 14924.4 17655.2 2730.8
102 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11068 8508.5 2559.5
p28 ing5. [refseq;acc:nm_032329] 0 2551.23 2243.69 307.54
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Divided 1442 977 1.47595
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 2353.63 3225.65 1.3705
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 0 630.942 327.517 303.425
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 1 11068 8508.5 2559.5
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Divided 0 197.333 290.667 1.47298
104 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 1 11068 8508.5 2559.5
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 4241.57 5810.79 1.36996
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] 0 5106.93 7500.75 1.46874
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Subtracted 688.436 385.626 302.81
105 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 5427.25 5130.58 296.67
fos-related antigen 2. [swissprot;acc:p15408] Divided 3233.86 2208.1 1.46454
musashi 1. [refseq;acc:nm_002442] 1 4241.57 5810.79 1.36996
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 11068 8508.5 2559.5
106 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 0 712.071 416.524 295.547
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 1 4241.57 5810.79 1.36996
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted 11068 8508.5 2559.5
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Divided 0 1251.66 858.525 1.45792
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1 4266.04 5843.51 1.36977
60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 0 1915.27 2206.07 290.8
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 326.677 472.605 1.4467
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted 1 14229.2 16780.7 2551.5
108 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Divided 0 292 421 1.44178
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1 4366.44 5899.76 1.35116
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Subtracted 0 482.426 192.295 290.131
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 1 14021.4 11523 2498.4
109 44050 protein. [refseq;acc:nm_178832] 17385.9 14889.2 2496.7
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Divided 0 100 144 1.44
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 4366.44 5899.76 1.35116
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Subtracted 0 934.726 1222.89 288.164
110 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 528.5 816.5 288
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] 1 17385.9 14889.2 2496.7
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 4366.44 5899.76 1.35116
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 0 1833 2637 1.43863
111 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 1 4366.44 5899.76 1.35116
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 2965.5 2063 1.43747
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted 10247.8 10535 287.2
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 1 12365.2 14824.9 2459.7
112 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 2405.69
lats homolog 1. [refseq;acc:nm_004690] Divided 0 160 112.25 1.42539
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 1095.42 812.166 283.254
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 1 4366.44 5899.76 1.35116
113 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Subtracted 4800.81 7132.71 2331.9
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 4366.44 5899.76 1.35116

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/