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 401 to 450 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
201 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 241.828 267.346 25.518
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 240.133 211.382 1.13601
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 240.758 266.079 25.321
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 201.478 228.784 1.13553
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 240.758 266.078 25.32
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 201.515 228.752 1.13516
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 268.632 243.588 25.044
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 201.515 228.752 1.13516
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 268.635 243.592 25.043
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Divided 228.1 200.968 1.13501
206 40s ribosomal protein s15a. [swissprot;acc:p39027] Subtracted 241.411 266.414 25.003
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 228.085 201.006 1.13472
207 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 237.312 212.363 24.949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 285.684 252.234 1.13261
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Subtracted 240.782 265.717 24.935
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 285.684 252.234 1.13261
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 240.782 265.717 24.935
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 285.684 252.234 1.13261
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617]
rna-binding protein. [refseq;acc:nm_019027] Subtracted 237.302 212.41 24.892
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 285.684 252.234 1.13261
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616]
ns1-associated protein 1. [refseq;acc:nm_006372] Subtracted 237.302 212.41 24.892
213 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Divided 210.693 186.95 1.127
214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Subtracted 241.282 266.12 24.838
215 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 24.835
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Divided 112 126 1.125
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 226.471 201.769 24.702
217 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 24.682
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Divided 112 126 1.125
218 60s ribosomal protein l35. [swissprot;acc:p42766] Subtracted 242.333 266.999 24.666
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided 112 126 1.125
219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 242.339 266.986 24.647
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided 112 126 1.125
220 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted 242.339 266.986 24.647
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 112 126 1.125
221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 242.627 267.151 24.524
222 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 24.52
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided 112 126 1.125
223 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Subtracted 242.153 266.673 24.52
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 185.969 165.623 1.12285
225 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted 242.153 266.673 24.52
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 226.471 201.769 1.12243

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/