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 651 to 700 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
326 60s ribosomal protein l5. [swissprot;acc:p46777] High confidence 241.899 265.924 1.09932
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Low confidence 199.343 191.59 1.04047
327 bet3 homolog. [swissprot;acc:o43617] 197.221 189.574 1.04034
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] High confidence 243.817 267.962 1.09903
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 203.162 195.289 1.04031
329 exocyst complex component exo70. [swissprot;acc:q9upt5] 204.124 212.339 1.04025
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 312 284 1.09859
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Low confidence 221.437 212.889 1.04015
331 doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 312 284 1.09859
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Low confidence 200.249 192.535 1.04007
332 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 209.495 201.474 1.03981
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 312 284 1.09859
333 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Low confidence 200.482 208.446 1.03972
334 coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] 202.616 194.878 1.03971
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 312 284 1.09859
335 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Low confidence 202.616 194.878 1.03971
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 312 284 1.09859
336 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Low confidence 202.616 194.878 1.03971
337 60s ribosomal protein l12. [swissprot;acc:p30050] High confidence 243.583 267.527 1.0983
serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Low confidence 201.873 194.181 1.03961
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] High confidence 243.583 267.528 1.0983
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Low confidence 202.572 194.86 1.03958
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] High confidence 243.583 267.527 1.0983
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Low confidence 209.518 201.554 1.03951
340 blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] 201.827 194.178 1.03939
myelin gene expression factor 2. [refseq;acc:nm_016132] High confidence 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Low confidence 214.027 222.415 1.03919
342 40s ribosomal protein s20. [swissprot;acc:p17075] High confidence 243.5 267.21 1.09737
tho complex 3. [refseq;acc:nm_032361] Low confidence 186.383 179.374 1.03907
343 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 213.982 222.326 1.03899
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] High confidence 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
mitochondrial ribosomal protein l44. [refseq;acc:nm_022915] Low confidence 216.283 208.173 1.03896
345 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] 213.976 222.312
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] High confidence 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Low confidence 209.221 201.38 1.03894
347 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] High confidence 242.14 265.697 1.09729
nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8] Low confidence 210.796 202.935 1.03874
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] High confidence 242.14 265.696 1.09728
spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] Low confidence 210.796 202.935 1.03874
349 adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973] 204.762 197.135 1.03869
surfeit locus protein 5. [swissprot;acc:q15528] High confidence 242.14 265.696 1.09728
350 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Low confidence 204.762 197.135 1.03869
zinc finger protein 291. [swissprot;acc:q9by12] High confidence 242.14 265.696 1.09728

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/