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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Value Type Gene Rank Interaction Map description Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2730 to 2779 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
863 neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Divided 5595.65 6173.23 1.10322
864 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 4682.87 4093.05 589.82
ring finger protein 44. [refseq;acc:nm_014901] Divided 5595.65 6173.23 1.10322
865 15 kda selenoprotein precursor. [swissprot;acc:o60613] Subtracted 6344.41 6933.36 588.95
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Divided 5595.65 6173.23 1.10322
866 nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Subtracted 4510.61 5098.74 588.13
ring finger protein 38. [refseq;acc:nm_022781] Divided 5595.65 6173.23 1.10322
867 phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Subtracted 6545.19 7132.89 587.7
868 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] 5607.43 6194.98 587.55
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Divided 5595.65 6173.23 1.10322
869 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Subtracted 6540.61 7127.41 586.8
870 phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Divided 5595.65 6173.23 1.10322
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Subtracted 6390.28 6973.08 582.8
871 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 581.42
protein bap28. [swissprot;acc:q9h583] Divided 3956.25 4364.25 1.10313
872 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] 6781.05 7480.15 1.1031
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Subtracted 6152.88 6732.12 579.24
873 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Divided 4749.52 5237.77 1.1028
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Subtracted 6607.68 7186.45 578.77
874 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Divided 9921.43 10941.2 1.10278
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Subtracted 6606.3 7185.01 578.71
875 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 6604.44 7183.07 578.63
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Divided 10263.8 11318.6 1.10277
876 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 5644.68 6223.23 1.10249
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Subtracted 9946.21 9367.66 578.55
877 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Divided 5797.88 6391.75 1.10243
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Subtracted 5644.68 6223.23 578.55
878 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided 5797.88 6391.75 1.10243
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Subtracted 6600.36 7178.84 578.48
879 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Divided 5797.88 6391.75 1.10243
ran binding protein 11. [refseq;acc:nm_016338] Subtracted 6138.91 6717.05 578.14
880 membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] 6136.99 6714.98 577.99
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Divided 5166.04 5694.55 1.1023
881 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 1.10229
neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Subtracted 5595.65 6173.23 577.58
882 ring finger protein 44. [refseq;acc:nm_014901]
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Divided 5912.84 6517.69 1.10229
883 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Subtracted 5595.65 6173.23 577.58
884 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Divided 5167.15 5695.44 1.10224
ring finger protein 38. [refseq;acc:nm_022781] Subtracted 5595.65 6173.23 577.58
885 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Divided 5168.01 5696.12 1.10219
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Subtracted 5595.65 6173.23 577.58
886 sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Divided 5903.18 6506.32 1.10217
887 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Subtracted 5595.65 6173.23 577.58
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Divided 5903.18 6506.32 1.10217
888 lbp-9. [refseq;acc:nm_014553]

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/