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 2530 to 2579 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
633 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided High confidence 234.106 248.104 1.05979
dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] Subtracted Low confidence 200.085 194.301 5.784
pp1201 protein. [refseq;acc:nm_022152] Divided 203.734 197.956 1.02919
634 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] High confidence 226.523 213.786 1.05958
pp1201 protein. [refseq;acc:nm_022152] Subtracted Low confidence 203.734 197.956 5.778
synapsin i (brain protein 4.1). [swissprot;acc:p17600] High confidence 229.072 216.576 12.496
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Divided Low confidence 203.726 197.955 1.02915
635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] High confidence 228.639 242.258 1.05957
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Low confidence 207.763 201.882 1.02913
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted High confidence 235.296 247.673 12.377
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Low confidence 203.726 197.955 5.771
636 probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] Divided 206.001 200.193 1.02901
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 204.933 199.164 5.769
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Divided High confidence 228.639 242.258 1.05957
vav proto-oncogene. [swissprot;acc:p15498] Subtracted 212.2 199.849 12.351
637 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] Divided Low confidence 192.166 186.751 1.029
amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] High confidence 228.639 242.258 1.05957
ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Subtracted Low confidence 208.62 202.855 5.765
vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 199.908 12.345
638 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Divided Low confidence 203.825 198.081 1.029
sorting nexin 17. [swissprot;acc:q15036] High confidence 228.639 242.258 1.05957
surfeit locus protein 1. [swissprot;acc:q15526] Subtracted Low confidence 201.211 195.459 5.752
vav-2 protein. [swissprot;acc:p52735] High confidence 212.526 200.212 12.314
639 nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Divided 217.67 230.596 1.05938
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Low confidence 204.933 199.164 1.02897
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Subtracted High confidence 222.554 234.847 12.293
zinc finger protein 216. [swissprot;acc:o76080] Low confidence 184.361 178.613 5.748
640 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] High confidence 244.842 232.577 12.265
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided 217.67 230.596 1.05938
megf6 (fragment). [sptrembl;acc:o75095] Low confidence 207.235 201.402 1.02896
protein associated with prk1. [refseq;acc:nm_019006] Subtracted 184.361 178.613 5.748
641 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] High confidence 244.842 232.577 12.265
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Low confidence 203.825 198.081 5.744
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided High confidence 217.67 230.596 1.05938
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 198.493 192.907 1.02896
642 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 203.883 198.148 1.02894
Subtracted 5.735
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Divided High confidence 217.67 230.596 1.05938
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Subtracted 228.944 216.745 12.199
643 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided Low confidence 203.104 197.399 1.0289
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] High confidence 217.67 230.596 1.05938
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
zinc finger protein t86. [swissprot;acc:o00488] Low confidence 205.897 200.163 5.734
644 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided High confidence 217.67 230.596 1.05938
integrin beta-7 precursor. [swissprot;acc:p26010] Subtracted Low confidence 206.341 200.609 5.732
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] High confidence 226.497 214.355 12.142
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided Low confidence 203.911 198.193 1.02885
645 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] High confidence 217.67 230.596 1.05938
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Subtracted 226.497 214.355 12.142
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Low confidence 206.342 200.61 5.732

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/