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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 375 to 424 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
188 60s ribosomal protein l15. [swissprot;acc:p39030] 0 11745.2 13203.1 1.12413
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 1 226.582 198.444 1.14179
189 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 0 10634.4 9465 1.12355
190 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 18809.5 16764.2 1.122
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 1 226.582 198.444 1.14179
191 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 0 18809.5 16764.2 1.122
192 musashi 2 isoform a. [refseq;acc:nm_138962] 1 227.491 199.458 1.14055
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] 0 12715.9 11333.2 1.122
193 musashi 1. [refseq;acc:nm_002442] 1 227.491 199.458 1.14055
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] 0 10899.5 12217.4 1.12091
194 kappa b-ras 1. [refseq;acc:nm_020345] 12657.7 11299.1 1.12024
nuclear protein ukp68. [refseq;acc:nm_024824] 1 227.491 199.458 1.14055
195 huntingtin interacting protein c. [refseq;acc:nm_012272] 227.971 200.417 1.13748
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 0 13942.8 15586.4 1.11788
196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1 263.215 231.407 1.13745
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 0 11064.2 9897.84 1.11784
197 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 1 263.215 231.407 1.13745
importin 4. [refseq;acc:nm_024658] 0 12337.6 13788.9 1.11763
198 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 1 263.191 231.394 1.13741
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 0 11781.5 10545.3 1.11723
199 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 11781.8 10545.7 1.11721
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 1 242.735 276.059 1.13729
200 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 242.718 276.018 1.1372
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 0 8786.74 7870.3 1.11644
201 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 16853 15123 1.1144
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 240.133 211.382 1.13601
202 serpin b11. [swissprot;acc:q96p15] 0 16853 15123 1.1144
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1 201.478 228.784 1.13553
203 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 0 16853 15123 1.1144
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 1 201.515 228.752 1.13516
204 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 15081.8 16802.1 1.11406
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 1 201.515 228.752 1.13516
205 60s ribosomal protein l23a. [swissprot;acc:p29316] 0 11844.9 10636.3 1.11363
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1 228.1 200.968 1.13501
206 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 0 7479 6716 1.11361
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1 228.085 201.006 1.13472
207 dc11 protein. [refseq;acc:nm_020186] 0 7479 6716 1.11361
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 1 285.684 252.234 1.13261
208 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 0 11846.3 10638.4 1.11354
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] 1 285.684 252.234 1.13261
209 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]
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 775 696 1.11351
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 285.684 252.234 1.13261
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 17144.8 15405.6 1.11289
211 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 285.684 252.234 1.13261
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 10367 9320.25 1.11231
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 285.684 252.234 1.13261
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 0 18241.7 16405 1.11196

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/