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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Filtered Value Type green description Interaction Map network_comparison Gene Rank red Network Comparison Type
Results: HTML CSV LaTeX Showing element 551 to 600 of 38536 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
green
description
Interaction Map
network_comparison
Rank
red
1068.02 myoglobin. [swissprot;acc:p02144] Low confidence 1.03554 605 1105.98
1070.03 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] High confidence 1.07338 339 996.883
1079.01 keratin associated protein 9.2. [refseq;acc:nm_031961] 1.13574 241 1225.47
1079.36 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 1.13502 247 1225.09
keratin associated protein 1.5. [refseq;acc:nm_031957] 245
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 244
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 243
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 246
1079.37 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 1.135 248
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 249 1225.08
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 250
1079.38 espin. [refseq;acc:nm_031475] 1.13498 253 1225.07
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 251 1225.08
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 252
1079.77 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 1.13418 256 1224.65
1081.5 small edrk-rich factor 1a. [swissprot;acc:o75920] Low confidence 1.21683 177 1316
1083.48 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] 1.02198 676 1107.29
1084.24 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 1.05021 563 1032.4
1084.89 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 1.02165 680 1108.38
1086.73 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 1.06522 482 1020.19
1087.6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 1.05215 554 1144.32
1094.3 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 1.03209 622 1129.42
1096.71 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 1.08668 429 1191.77
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 430
1099.49 jm5 protein. [refseq;acc:nm_007075] 1.1204 366 981.333
1104.61 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] High confidence 1.09796 315 1212.82
1106.88 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 1.62908 85 679.449
1107 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 1.24887 175 1382.5
Low confidence 162
1117.07 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1.19475 190 934.98
1117.36 kappa b-ras 1. [refseq;acc:nm_020345] High confidence 1.03203 422 1153.15
1119.1 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Low confidence 1.13701 345 1272.43
1122.57 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 1.22602 170 915.62
1134.29 ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39] 1.05755 515 1199.57
1135.73 40s ribosomal protein s10. [swissprot;acc:p46783] 1.05788 513 1201.47
1139 cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035] 1.3032 133 874
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] High confidence 142
Low confidence 134
1148.47 timeless homolog. [refseq;acc:nm_003920] 1.00239 817 1151.21
1149.89 my016 protein. [sptrembl;acc:q9h3k6] 1.06837 477 1228.51
1150.51 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] High confidence 1.3267 136 1526.38
1152.06 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] 1.27473 161 903.767
1161.29 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1.02978 427 1195.87
1161.64 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1.11371 288 1293.73
Low confidence 382
1161.99 transmembrane 6 superfamily member 2 (fragment). [swissprot;acc:q9bzw4] 1.11685 373 1297.77
1162.04 hyaluronan and proteoglycan link protein 3. [refseq;acc:nm_178232] 374 1297.83
1162.87 versican core protein precursor (large fibroblast proteoglycan) (chondroitin sulfate proteoglycan core protein 2) (pg-m) (glial hyaluronate-binding protein) (ghap). [swissprot;acc:p13611] 1.11694 372 1298.86
1165.27 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1.01153 759 1151.99
1171 mitochondrial 39s ribosomal protein l39 (l39mt) (mrp-l39) (mrp-l5) (pred22 protein). [swissprot;acc:q9nyk5] 1.06618 481 1248.5

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/