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 2251 to 2300 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1126 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Divided 218.487 212.656 1.02742
snare associated protein snapin. [refseq;acc:nm_012437] Subtracted 220.758 215.097 5.661
1127 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Divided 239.219 232.837 1.02741
sorting nexin 1. [swissprot;acc:q13596] Subtracted 209.868 215.522 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] 187.96 182.308 5.652
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Divided 221.286 215.399 1.02733
1129 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] 221.285 215.401 1.02732
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Subtracted 258.558 252.916 5.642
1130 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Divided 221.285 215.4 1.02732
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Subtracted 187.022 181.391 5.631
1131 transducin-like enhancer protein 4. [swissprot;acc:q04727] 219.438 213.818 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 218.484 212.675 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 225.906 231.524 5.618
1133 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 210.022
sec13-related protein. [swissprot;acc:p55735] Divided 218.484 212.675 1.02731
1134 transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Subtracted 219.401 213.785 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 218.484 212.675 1.02731
1135 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Subtracted 219.399 213.784 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 218.484 212.675 1.02731
1136 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Subtracted 219.399 213.784 5.615
yeast sec31p homolog. [refseq;acc:nm_014933] Divided 218.484 212.675 1.02731
1137 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Subtracted 219.399 213.784 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 218.484 212.675 1.02731
1138 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Subtracted 219.399 213.784 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 218.484 212.675 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 219.374 213.759 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 218.484 212.675 1.02731
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Subtracted 219.399 213.784 5.615
1141 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] Divided 218.484 212.675 1.02731
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Subtracted 219.375 213.767 5.608
1142 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 216.729 222.334 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 218.484 212.675 1.02731
1143 kinesin protein. [refseq;acc:nm_032559] Subtracted 224.858 219.264 5.594
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Divided 218.484 212.675 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 135.844 130.259 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 218.484 212.675 1.02731
1145 ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Subtracted 224.805 219.251 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 218.481 212.675 1.0273
1146 ubiquitin. [swissprot;acc:p02248] Subtracted 209.061 203.518 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 218.483 212.676 1.0273
1147 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 208.651 203.109 1.02729
Subtracted 5.542
1148 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 224.878 219.342 5.536
ubiquitin. [swissprot;acc:p02248] Divided 209.061 203.518 1.02724
1149 bystin. [swissprot;acc:q13895] 239.505 233.185 1.0271
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Subtracted 224.764 219.241 5.523
1150 sorting nexin 1. [swissprot;acc:q13596] Divided 209.868 215.522 1.02694
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Subtracted 218.186 212.672 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/