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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 2301 to 2350 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
network_comparison
red
green
288 Subtracted no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Rooted 8.068 55.8956 63.9636
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared 7870.8 28896.2 36767
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 22.751 234.691 257.442
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Measured 1182.34 4069.83 5252.17
289 Divided no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 1.10486 272.781 246.892
KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 1.27956 6693.64 8564.94
LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured 1.20571 4682.88 5646.19
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 1.11899 57.4274 64.2609
Subtracted ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared 7870.8 28896.2 36767
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Measured 1182.34 4069.83 5252.17
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Rooted 8.068 55.8956 63.9636
STX6 syntaxin 6. [swissprot;acc:o43752] Ranked 22.741 234.673 257.414
290 Divided no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Rooted 1.11788 75.6323 67.6572
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared 1.27916 15734.4 20126.8
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked 1.10428 231.969 210.064
TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Measured 1.20487 4991.48 6014.08
Subtracted no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared 7870.8 28896.2 36767
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Ranked 22.681 242.109 264.79
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Measured 1180.65 4071.1 5251.75
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted 8.0316 66.1122 74.1438
291 Divided no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 1.11771 113.983 101.979
CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 1.27909 59016.1 75486.9
NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Ranked 1.10368 251.679 228.037
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured 1.20481 44490.5 36927.5
Subtracted AK2 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] Ranked 22.654 241.509 264.163
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 8.001 66.1064 74.1074
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 7870.8 28896.2 36767
PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured 1178.9 5894.75 7073.65
292 Divided LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Rooted 1.11755 56.48 63.119
NEURL neuralized-like. [refseq;acc:nm_004210] Squared 1.27831 6828.26 8728.66
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 1.20419 4641.09 5588.75
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 1.10357 241.411 266.414
Subtracted no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 8.001 66.1064 74.1074
CRKL crk-like protein. [swissprot;acc:p46109] Squared 7870.8 28896.2 36767
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 22.481 234.146 256.627
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 1157.96 950.561 2108.52
293 Divided no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Ranked 1.10356 240.782 265.717
KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 1.27815 35991.8 46002.9
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured 1.20419 4641.09 5588.75
TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Rooted 1.11729 63.0715 56.4506
Subtracted no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 1143.33 4512.19 5655.52
ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 7870.8 28896.2 36767
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 8.001 66.1064 74.1074
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 22.443 219.421 196.978
294 Divided AGPAT2 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Squared 1.2776 30826.5 39383.9
BCCIP 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] Ranked 1.10356 240.782 265.717
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 1.20387 22515.5 18702.6
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 1.11725 59.0296 65.951
Subtracted CRKL crk-like protein. [swissprot;acc:p46109] 8.001 66.1064 74.1074
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 7870.8 28896.2 36767

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/