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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 2251 to 2300 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1126 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Divided 212.656 218.487 1.02742
snare associated protein snapin. [refseq;acc:nm_012437] Subtracted 215.097 220.758 5.661
1127 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Divided 232.837 239.219 1.02741
sorting nexin 1. [swissprot;acc:q13596] Subtracted 215.522 209.868 5.654
1128 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 182.308 187.96 5.652
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Divided 215.399 221.286 1.02733
1129 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 215.401 221.285 1.02732
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Subtracted 252.916 258.558 5.642
1130 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Divided 215.4 221.285 1.02732
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Subtracted 181.391 187.022 5.631
1131 transducin-like enhancer protein 4. [swissprot;acc:q04727] 213.818 219.438 5.62
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] Divided 212.675 218.484 1.02731
1132 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Subtracted 231.524 225.906 5.618
1133 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 210.022 204.404
sec13-related protein. [swissprot;acc:p55735] Divided 212.675 218.484 1.02731
1134 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Subtracted 213.785 219.401 5.616
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Divided 212.675 218.484 1.02731
1135 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted 213.784 219.399 5.615
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Divided 212.675 218.484 1.02731
1136 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Subtracted 213.784 219.399 5.615
yeast sec31p homolog. [refseq;acc:nm_014933] Divided 212.675 218.484 1.02731
1137 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted 213.784 219.399 5.615
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Divided 212.675 218.484 1.02731
1138 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Subtracted 213.784 219.399 5.615
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Divided 212.675 218.484 1.02731
1139 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Subtracted 213.759 219.374 5.615
1140 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Divided 212.675 218.484 1.02731
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Subtracted 213.784 219.399 5.615
1141 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Divided 212.675 218.484 1.02731
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Subtracted 213.767 219.375 5.608
1142 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 222.334 216.729 5.605
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Divided 212.675 218.484 1.02731
1143 kinesin protein. [refseq;acc:nm_032559] Subtracted 219.264 224.858 5.594
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Divided 212.675 218.484 1.02731
1144 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 130.259 135.844 5.585
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Divided 212.675 218.484 1.02731
1145 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Subtracted 219.251 224.805 5.554
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Divided 212.675 218.481 1.0273
1146 ubiquitin. [swissprot;acc:p02248] Subtracted 203.518 209.061 5.543
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Divided 212.676 218.483 1.0273
1147 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 203.109 208.651 1.02729
Subtracted 5.542
1148 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 219.342 224.878 5.536
ubiquitin. [swissprot;acc:p02248] Divided 203.518 209.061 1.02724
1149 bystin. [swissprot;acc:q13895] 233.185 239.505 1.0271
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Subtracted 219.241 224.764 5.523
1150 sorting nexin 1. [swissprot;acc:q13596] Divided 215.522 209.868 1.02694
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Subtracted 212.672 218.186 5.514

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/