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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1962 to 2011 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
246 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided Rooted 146.94 1.13683 167.046
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted 27.9136 9.3736 37.2872
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 13241.4 1377.4 11864
EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Divided Ranked 237.312 1.11748 212.363
HHEX homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Subtracted Squared 54726.7 9368.2 45358.5
HOMER3 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Divided Measured 4252.66 1.22583 5213.05
PYGB glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 1.31131 6768.05
247 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Subtracted Ranked 243.583 23.944 267.527
rna-binding protein. [refseq;acc:nm_019027] Divided 237.302 1.11719 212.41
DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 1.13668 53.8355
FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Subtracted Measured 13241.4 1377.4 11864
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Rooted 27.9136 9.3736 37.2872
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 9176.8 43159.1
PYGL glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Divided 8875.01 1.31131 6768.05
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 1.22574 7865.15
248 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 1.11719 212.41
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 243.583 23.944 267.527
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Divided Measured 6417.18 1.22477 7859.6
IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Subtracted Squared 37226.9 9173.2 46400.1
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided Rooted 56.0466 1.13264 63.4808
MYO15A myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 8875.01 1.31131 6768.05
NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted Rooted 27.9136 9.3736 37.2872
PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Measured 13241.4 1377.4 11864
249 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 6417.18 1.22477 7859.59
BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 1.13199 62.9349
CDC23 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Subtracted Squared 51616.7 9027.8 42588.9
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Rooted 27.9136 9.3736 37.2872
PYGM glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Divided Squared 8875.01 1.31131 6768.05
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted Measured 4405.4 1376.68 5782.08
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 226.109 23.776 202.333
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Divided 237.302 1.11719 212.41
250 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 1.22477 7859.6
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted Rooted 27.9136 9.3736 37.2872
CTBP2 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Divided Squared 69201.8 1.30536 53013.4
HARS2 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Subtracted 34527.9 8980 43507.9
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided Ranked 237.302 1.11719 212.41
NOLA1 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 1.13199 62.9349
PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Subtracted Ranked 210.693 23.743 186.95
SH2D3C 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] Measured 4578.09 1361.82 5939.91
251 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 1361.3 5940.64
BCL6B b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Divided Squared 69165.6 1.30521 52992.1
CDK2AP1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Subtracted Rooted 27.9136 9.3736 37.2872
HARS histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 8969.7 43476
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided Measured 6417.18 1.22477 7859.6
MAX max protein. [swissprot;acc:p25912] Rooted 56.3054 1.13159 63.7148
RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Subtracted Ranked 243.5 23.71 267.21
SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 186.172 1.11707 166.661
252 CENPJ centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Subtracted Squared 51286.6 8952.1 42334.5
CRKL crk-like protein. [swissprot;acc:p46109] Divided Measured 6417.18 1.22477 7859.6
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 1.11689 212.457

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/