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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2230 to 2279 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1115 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Divided 251.863 258.829 1.02766
1116 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Subtracted 204.603 210.324 5.721
1117 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Divided 168.989 164.46 1.02754
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Subtracted 186.551 180.837 5.714
1118 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] 221.877 216.167 5.71
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Divided 168.995 164.467 1.02753
1119 peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Subtracted 207.553 213.256 5.703
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Divided 218.528 212.676 1.02752
1120 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Subtracted 186.741 181.041 5.7
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] Divided 218.528 212.676 1.02752
1121 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Subtracted 187.834 182.137 5.697
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Divided 218.529 212.676 1.02752
1122 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Subtracted 186.774 181.099 5.675
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Divided 218.527 212.676 1.02751
1123 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Subtracted 186.799 181.127 5.672
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Divided 169.031 164.507 1.0275
1124 kappa b-ras 1. [refseq;acc:nm_020345] Subtracted 220.758 215.097 5.661
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Divided 207.553 213.256 1.02748
1125 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 204.404 210.022
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Subtracted 220.758 215.097 5.661
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

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/