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 1400 to 1449 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
700 vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Subtracted 5768.32 6434.78 666.46
701 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326]
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Divided 7802.31 8731.82 1.11913
702 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 7067.46 7909.27 1.11911
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted 5549.2 6215.42 666.22
703 nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Divided 6912.56 7735.12 1.11899
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Subtracted 5549.2 6215.42 666.22
704 alpha-nac protein. [sptrembl;acc:q9h009] Divided 6912.27 7734.68 1.11898
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Subtracted 5549.2 6215.42 666.22
705 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Divided 6912.09 7734.41 1.11897
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Subtracted 5549.2 6215.42 666.22
706 di-ras2. [refseq;acc:nm_017594] Divided 6912.08 7734.39 1.11897
syntaxin 12. [refseq;acc:nm_177424] Subtracted 5552.92 6217.59 664.67
707 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 5870.2 6533.39 663.19
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Divided 5317.78 5944.25 1.11781
708 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Subtracted 4775.11 5438.18 663.07
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Divided 5317.78 5944.25 1.11781
709 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Subtracted 5148.71 5811.74 663.03
pp1201 protein. [refseq;acc:nm_022152] Divided 5317.78 5944.25 1.11781
710 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Subtracted 2755.15 2094.3 660.85
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Divided 5317.78 5944.25 1.11781
711 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Subtracted 2759.61 2099.49 660.12
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided 5317.78 5944.25 1.11781
712 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Subtracted 2760.28 2100.27 660.01
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Divided 5317.78 5944.25 1.11781
713 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted 5162.52 5822.47 659.95
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Divided 3996.81 4465.61 1.11729
714 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 5222.71 5834.57 1.11715
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] Subtracted 5873.77 6532.44 658.67
715 dendritic cell protein. [refseq;acc:nm_006360] Divided 6593.17 7364.55 1.117
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] Subtracted 5874.74 6533.34 658.6
716 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Divided 6593.17 7364.55 1.117
717 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
sec13-related protein. [swissprot;acc:p55735] Subtracted 5874.76 6533.36 658.6
718 cpz gene product. [refseq;acc:nm_003652] Divided 6593.17 7364.55 1.117
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] Subtracted 5874.74 6533.34 658.6
719 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Divided 6593.17 7364.55 1.117
yeast sec31p homolog. [refseq;acc:nm_014933] Subtracted 5874.76 6533.36 658.6
720 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Divided 6593.17 7364.55 1.117
721 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Subtracted 5874.74 6533.34 658.6
syntaxin 7. [swissprot;acc:o15400] Divided 5580.97 6233.52 1.11692
722 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 8061.05 9002.33 1.11677
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] Subtracted 5874.63 6533.23 658.6
723 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Divided 8056.09 8996.46 1.11673
724 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 5384.41 6012.82 1.11671
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] Subtracted 5874.76 6533.36 658.6
725 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 5384.41 6012.82 1.11671

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/