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 2808 to 2857 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
351 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Ranked Subtracted 233.376 253.539 20.163
352 40s ribosomal protein s28. [swissprot;acc:p25112] Squared Divided 30682.9 38183.6 1.24446
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted 42467.5 36156.7 6310.8
bet3 homolog. [swissprot;acc:o43617] Measured Divided 17396.9 20483.9 1.17745
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted 61.3354 67.8621 1.10641
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 242.14 265.696 1.09728
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 237.862 217.739 20.123
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 6.8382
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 5909.18 997.37
353 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 6305.1
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Divided 71383 57399.3 1.24362
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Subtracted 94 114 20
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Measured 4911.81 5909.18 997.37
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Rooted Divided 61.3354 67.8623 1.10641
p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1.17669
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted Subtracted 57.4274 64.2609 6.8335
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Ranked Divided 231.73 211.252 1.09694
354 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared Subtracted 34129.6 40434.5 6304.9
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 6.8086
paraspeckle protein 1. [refseq;acc:nm_018282] Squared Divided 71360.3 57385.8 1.24352
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked Subtracted 94 114 20
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Measured 6913.6 7907.05 993.45
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked Divided 234.691 257.442 1.09694
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1.17669
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 1.10632
355 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Squared Subtracted 34129.6 40434.5 6304.9
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked 94 114 20
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Measured 4914.27 5907.12 992.85
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Rooted 50.2801 43.4779 6.8022
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 58.0752 64.23 1.10598
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Squared 15588.1 19381.8 1.24337
syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 257.414 1.09691
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured 12839 10911.1 1.17669
356 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared Subtracted 34129.6 40434.5 6304.9
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked Divided 243.24 266.796 1.09684
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 94 114 20
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared Divided 35247.5 43820.5 1.24322
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Rooted 58.0752 64.23 1.10598
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 12944.2 1.1763
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted 4914.27 5907.12 992.85
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 6.7971
357 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Squared 34129.6 40434.5 6304.9
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Ranked Divided 243.12 266.661 1.09683
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted 61.2684 67.755 1.10587
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured 5061.11 5950.22 1.17567
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Ranked Subtracted 94 114 20
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 989.35
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Rooted 46.3291 53.1063 6.7772
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared Divided 9811.86 7908.29 1.24071
358 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Subtracted 34129.6 40434.5 6304.9

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/