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 863 to 912 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
216 neuromedin-b receptor (nmb-r) (neuromedin-b-preferring bombesin receptor). [swissprot;acc:p28336] Divided Low confidence 199.671 209.654 1.05
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted High confidence 226.471 201.769 24.702
217 60s ribosomal protein l26. [swissprot;acc:q02877] 242.326 267.008 24.682
gastrin-releasing peptide receptor (grp-r) (grp-preferring bombesin receptor). [swissprot;acc:p30550] Divided Low confidence 199.671 209.654 1.05
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] High confidence 112 126 1.125
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Subtracted Low confidence 206.583 196.743 9.84
218 60s ribosomal protein l35. [swissprot;acc:p42766] High confidence 242.333 266.999 24.666
bombesin receptor subtype-3 (brs-3). [swissprot;acc:p32247] Divided Low confidence 199.671 209.654 1.05
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Subtracted 208.289 198.538 9.751
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Divided High confidence 112 126 1.125
219 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Subtracted 242.339 266.986 24.647
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Low confidence 214.032 204.284 9.748
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Divided High confidence 112 126 1.125
transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Low confidence 172.647 164.44 1.04991
220 mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Subtracted High confidence 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
nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence 172.647 164.44 1.04991
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Subtracted 207.926 198.276 9.65
221 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Divided High confidence 112 126 1.125
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 242.627 267.151 24.524
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 189.373 179.829 9.544
transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Divided 172.647 164.44 1.04991
222 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Subtracted High confidence 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
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted Low confidence 212.056 202.524 9.532
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Divided 203.935 214.089 1.04979
223 general transcription factor iiic, polypeptide 3, 102kda; general transcription factor iiic, polypeptide 3 (102kd); transcription factor iiic, 102 kd. [refseq;acc:nm_012086] 217.228 206.926
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] High confidence 112 126 1.125
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Subtracted 242.153 266.673 24.52
single-minded homolog 1. [swissprot;acc:p81133] Low confidence 212.056 202.524 9.532
224 60s ribosomal protein l34. [swissprot;acc:p49207] High confidence 242.153 266.673 24.52
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Low confidence 209.649 200.129 9.52
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Divided High confidence 185.969 165.623 1.12285
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Low confidence 203.933 214.059 1.04965
225 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Subtracted 216.855 207.34 9.515
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 201.41 191.974 1.04915
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted High confidence 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
226 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Subtracted Low confidence 216.845 207.333 9.512
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Divided High confidence 239.991 269.238 1.12187
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Low confidence 208.289 198.538 1.04911
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Subtracted High confidence 242.153 266.673 24.52
227 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Low confidence 216.842 207.332 9.51
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Divided 216.404 206.277 1.04909
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Subtracted High confidence 244.126 268.604 24.478
thrombospondin 3 precursor. [swissprot;acc:p49746] Divided 239.99 269.234 1.12186
228 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Subtracted 244.126 268.604 24.478
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 189.45 179.944 9.506
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Divided High confidence 226.411 202.088 1.12036
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] Low confidence 202.727 193.31 1.04871

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/