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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1701 to 1750 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1701 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] G6PD 216.079 219.024 1.01363
1702 dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] XRCC3
1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] RECQL5
1704 ataxin 2-binding protein. [swissprot;acc:q9nwb1] no value 218.514 215.577 1.01362
1705 serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] PPP4C 223.846 220.847 1.01358
1706 immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] IGBP1
1707 mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] BUB1B 221.283 218.334 1.01351
1708 pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] PNPO
1709 homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] HHEX 198.014 195.385 1.01346
1710 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] no value 227.225 224.21 1.01345
1711 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] HLCS 218.436 215.553 1.01337
1712 transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] TAF11 208.598 211.375 1.01331
1713 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] SH3GL3 206.823 204.111 1.01329
1714 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] ARMET 206.549 203.844 1.01327
1715 histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] HDC
1716 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] SH3GL2 206.522 203.818
1717 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] OSGEP 221.058 218.164
1718 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] SH3GL1 206.251 203.553 1.01325
1719 helicase (fragment). [sptrembl;acc:q92771] no value 187.204 189.679 1.01322
1720 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] DDX12 187.205
1721 casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] CSNK1D 227.125 224.164 1.01321
1722 40s ribosomal protein s13. [swissprot;acc:q02546] RPS13 220.899 223.813 1.01319
1723 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] NADK 212.36 215.147 1.01312
1724 inositol polyphosphate multikinase. [refseq;acc:nm_152230] IPMK 217.676 220.53 1.01311
1725 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] AFG3L2
1726 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] FUT8
1727 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] IMPA1 210.366 213.118 1.01308
1728 inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] IMPA2 210.358 213.103 1.01305
1729 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] ATG12 187.582 190.028 1.01304
1730 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] CABC1 215.336 212.567 1.01303
1731 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] ADCK2
1732 aarf domain containing kinase 4. [refseq;acc:nm_024876] ADCK4
1733 aarf domain containing kinase 1. [refseq;acc:nm_020421] ADCK1
1734 nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] NOLA2 221.921 219.081 1.01296
1735 leucyl-trna synthetase. [refseq;acc:nm_020117] LARS 218.99 216.189
1736 transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] GTF2F1 221.921 219.081
1737 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] LARS2 218.99 216.189
1738 lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] LIPT1 206.595 209.258 1.01289
1739 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] TUBG1
1740 defender against cell death 1 (dad-1). [swissprot;acc:p46966] DAD1
1741 t-complex 11. [refseq;acc:nm_018679] TCP11
1742 tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] TUBG2
1743 pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] no value 218.176 215.402 1.01288
1744 sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] SGPL1 219.423 222.215 1.01272
1745 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] no value
1746 ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] OAT
1747 tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] ERCC2 188.452 190.845 1.0127
1748 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] no value 215.673 212.971 1.01269
1749 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] MLH3 206.058 203.485 1.01264
1750 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] LIMCH1 216.27 213.57

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/