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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2513 to 2562 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
629 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Divided High confidence 214.256 202.14 1.05994
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted Low confidence 204.242 198.448 5.794
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] High confidence 229.072 216.576 12.496
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Divided Low confidence 204.369 198.564 1.02923
630 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 204.242 198.448 5.794
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] High confidence 229.072 216.576 12.496
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Divided 214.256 202.141 1.05993
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Low confidence 204.369 198.564 1.02923
631 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 204.242 198.448 1.0292
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] High confidence 214.256 202.141 1.05993
similar to s. cerevisiae ssm4. [refseq;acc:nm_005885] Subtracted Low confidence 207.662 201.876 5.786
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] High confidence 229.072 216.576 12.496
632 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided Low confidence 204.242 198.448 1.0292
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] High confidence 214.254 202.166 1.05979
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted Low confidence 207.662 201.876 5.786
633 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] High confidence 229.072 216.576 12.496
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided 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

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/