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 Hugo 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
Hugo
Network Comparison Type
red
green
network_comparison
201 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 Subtracted 241.828 267.346 25.518
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Divided 240.133 211.382 1.13601
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] RPS4Y2 Subtracted 240.758 266.079 25.321
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] TRPC4 Divided 201.478 228.784 1.13553
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] no value Subtracted 240.758 266.078 25.32
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] TBC1D10A 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] CAPN2 Subtracted 268.632 243.588 25.044
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] TRPC5 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] CAPN1 Subtracted 268.635 243.592 25.043
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] LUC7L2 Divided 228.1 200.968 1.13501
206 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A Subtracted 241.411 266.414 25.003
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] LUC7L Divided 228.085 201.006 1.13472
207 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Subtracted 237.312 212.363 24.949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] PSEN2 Divided 285.684 252.234 1.13261
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value 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] SKP1A 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] BCCIP 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] FBXW7 Divided 285.684 252.234 1.13261
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617] CUL2
rna-binding protein. [refseq;acc:nm_019027] no value 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] PSEN1 Divided 285.684 252.234 1.13261
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616] CUL1
ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Subtracted 237.302 212.41 24.892
213 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Divided 210.693 186.95 1.127
214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 191.644 170.192 1.12605
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] MRPL4 Subtracted 241.282 266.12 24.838
215 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 237.292 212.457 24.835
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] no value Divided 112 126 1.125
216 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] MYH4
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 Subtracted 226.471 201.769 24.702
217 60s ribosomal protein l26. [swissprot;acc:q02877] RPL26 242.326 267.008 24.682
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] MYH8 Divided 112 126 1.125
218 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 Subtracted 242.333 266.999 24.666
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] MYH2 Divided 112 126 1.125
219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value Subtracted 242.339 266.986 24.647
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] MYH3 Divided 112 126 1.125
220 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] MRPL2 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] MYH1 Divided 112 126 1.125
221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] no value
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] EIF1B Subtracted 242.627 267.151 24.524
222 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] no value 242.153 266.673 24.52
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] MYH7B Divided 112 126 1.125
223 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] MYH13
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] SRR Subtracted 242.153 266.673 24.52
224 60s ribosomal protein l34. [swissprot;acc:p49207] RPL34
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] SLC15A2 Divided 185.969 165.623 1.12285
225 protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] SEC61A2 Subtracted 242.153 266.673 24.52
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] SNRPD2 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
- Hugo is the HGNC identifier if it exists
- 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/