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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 2330 to 2379 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
red
network_comparison
green
292 Divided NEURL neuralized-like. [refseq;acc:nm_004210] Squared 6828.26 1.27831 8728.66
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 4641.09 1.20419 5588.75
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 241.411 1.10357 266.414
Subtracted no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 66.1064 8.001 74.1074
CRKL crk-like protein. [swissprot;acc:p46109] Squared 28896.2 7870.8 36767
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 22.481 256.627
PRKRAP1 protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 950.561 1157.96 2108.52
293 Divided no value 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Ranked 240.782 1.10356 265.717
KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared 35991.8 1.27815 46002.9
NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured 4641.09 1.20419 5588.75
TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Rooted 63.0715 1.11729 56.4506
Subtracted no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 4512.19 1143.33 5655.52
ABL1 proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 7870.8 36767
HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 66.1064 8.001 74.1074
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Ranked 219.421 22.443 196.978
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 30826.5 1.2776 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 240.782 1.10356 265.717
CSTF3 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 22515.5 1.20387 18702.6
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 59.0296 1.11725 65.951
Subtracted CRKL crk-like protein. [swissprot;acc:p46109] 66.1064 8.001 74.1074
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 7870.8 36767
HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 219.421 22.443 196.978
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured 4512.19 1143.33 5655.52
295 Divided no value 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Squared 30807.7 1.27733 39351.7
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 1.11711 65.9421
RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured 13261.9 1.20368 11017.8
SCYE1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 1.103 202.423
Subtracted no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured 5720.25 1142.75 4577.5
FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 7870.8 36767
FYN proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 8.001 74.1074
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 22.443 196.978
296 Divided MRPL4 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 241.282 1.10294 266.12
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 1.20306 5909.18
TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Rooted 63.0663 1.11688 56.4667
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 1.27372 36783.5
Subtracted FGR proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 8.001 74.1074
GRAP2 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Squared 28896.4 7870.4 36766.8
HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked 219.421 22.443 196.978
NFYC 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] Measured 3620.77 1142.57 4763.34
297 Divided no value 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 1.1029 259.984
KLF5 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 1.20306 5909.18
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Squared 14247.4 1.27336 18142.1
TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 1.11688 56.4667
Subtracted ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 66.1064 8.0009 74.1073
CUTL1 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared 28900.8 7861.8 36762.6
DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 22.443 196.978
NFYA 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] Measured 3620.77 1142.57 4763.34
298 Divided no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Squared 14247.4 1.27336 18142.1
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured 4633.92 1.20262 5572.85
CAPN2 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] Ranked 268.632 1.10281 243.588

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/