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 Network Comparison Type Value Type Interaction Map Filtered green network_comparison red
Results: HTML CSV LaTeX Showing element 401 to 450 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
network_comparison
red
201 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 267.346 25.518 241.828
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 211.382 1.13601 240.133
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 266.079 25.321 240.758
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 228.784 1.13553 201.478
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 266.078 25.32 240.758
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 228.752 1.13516 201.515
204 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 243.588 25.044 268.632
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 228.752 1.13516 201.515
205 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 243.592 25.043 268.635
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 200.968 1.13501 228.1
206 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 266.414 25.003 241.411
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 201.006 1.13472 228.085
207 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 212.363 24.949 237.312
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 252.234 1.13261 285.684
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 265.717 24.935 240.782
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Divided 252.234 1.13261 285.684
209 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Subtracted 265.717 24.935 240.782
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Divided 252.234 1.13261 285.684
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
rna-binding protein. [refseq;acc:nm_019027] Subtracted 212.41 24.892 237.302
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided 252.234 1.13261 285.684
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 212.41 24.892 237.302
213 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 186.95 1.127 210.693
214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 170.192 1.12605 191.644
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted 266.12 24.838 241.282
215 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 24.835 237.292
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 126 1.125 112
216 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted 201.769 24.702 226.471
217 60s ribosomal protein l26. [swissprot;acc:q02877] 267.008 24.682 242.326
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Divided 126 1.125 112
218 60s ribosomal protein l35. [swissprot;acc:p42766] Subtracted 266.999 24.666 242.333
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 126 1.125 112
219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 266.986 24.647 242.339
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 126 1.125 112
220 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted 266.986 24.647 242.339
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 126 1.125 112
221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 267.151 24.524 242.627
222 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 266.673 24.52 242.153
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided 126 1.125 112
223 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Subtracted 266.673 24.52 242.153
224 60s ribosomal protein l34. [swissprot;acc:p49207]
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided 165.623 1.12285 185.969
225 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted 266.673 24.52 242.153
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 201.769 1.12243 226.471

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/