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 794 to 843 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
199 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 0 11781.8 10545.7 1.11721
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Subtracted 11846.3 10638.4 1207.9
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Divided 1 242.735 276.059 1.13729
200 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Subtracted 241.808 267.335 25.527
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 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
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 13483.3 14685.4 1202.1
201 60s ribosomal protein l11. [swissprot;acc:p39026] 1 241.828 267.346 25.518
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 6814 8009 1195
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Divided 16853 15123 1.1144
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 1 240.133 211.382 1.13601
202 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 240.758 266.079 25.321
serpin b11. [swissprot;acc:q96p15] Divided 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
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted 0 8214.41 7026.41 1188
203 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 1 240.758 266.078 25.32
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Divided 0 16853 15123 1.1144
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 1 201.515 228.752 1.13516
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted 0 12196.2 11009.7 1186.5
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] 1 268.632 243.588 25.044
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Divided 0 15081.8 16802.1 1.11406
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted 10559.7 11732 1172.3
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 1 201.515 228.752 1.13516
205 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 0 12183 11013.2 1169.8
60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 11844.9 10636.3 1.11363
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Subtracted 1 268.635 243.592 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
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Divided 0 7479 6716 1.11361
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1 228.085 201.006 1.13472
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 0 10634.4 9465 1169.4
207 dc11 protein. [refseq;acc:nm_020186] Divided 7479 6716 1.11361
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Subtracted 1 237.312 212.363 24.949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 285.684 252.234 1.13261
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 0 11064.2 9897.84 1166.36
208 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 1 240.782 265.717 24.935
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Divided 0 11846.3 10638.4 1.11354
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] Subtracted 19939 18778 1161
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 1 285.684 252.234 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
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 775 696 1.11351
tigger transposable element derived 6. [refseq;acc:nm_030953] Subtracted 12360 11200.2 1159.8
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Divided 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
rna-binding protein. [refseq;acc:nm_019027] Subtracted 1 237.302 212.41 24.892
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 0 12364.7 11207.7 1157
211 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 1 237.302 212.41 24.892
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Divided 285.684 252.234 1.13261
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 10367 9320.25 1.11231

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/