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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6091 to 6140 of 66312 in total
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
Interaction Map
red
green
network_comparison
381 SCYE1 Measured multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Divided High confidence 5246.01 6109.31 1.16456
SEL1L2 Rooted dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Subtracted Low confidence 74.9096 78.4542 3.5446
SLC16A10 solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593] Divided 84.0132 88.0936 1.04857
SLC46A2 Ranked thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted High confidence 248.152 267.226 19.074
STMN4 Squared stathmin 4 (stathmin-like protein b3) (rb3). [swissprot;acc:q9h169] Divided Low confidence 48784.9 45597.3 1.06991
TAF7 Ranked transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] High confidence 200.586 183.423 1.09357
382 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted Low confidence 162.755 155.476 7.279
Squared rna-binding protein. [refseq;acc:nm_019027] Divided High confidence 15043.7 18560.1 1.23375
CDKL1 Measured serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Subtracted Low confidence 7701.35 8143.34 441.99
COG7 Squared conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 51199.2 47994.4 3204.8
DDX54 Ranked atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] High confidence 253.852 234.808 19.044
HARS Measured histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Divided Low confidence 8721.03 9188.39 1.05359
IBTK Squared inhibitor of bruton's tyrsoine kinase; btk-binding protein. [refseq;acc:nm_015525] 48784.9 45597.3 1.06991
MXI1 Ranked max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 205.926 198.554 1.03713
PARK2 Measured parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] High confidence 4533.74 5279.4 1.16447
RPS23 Rooted 40s ribosomal protein s23. [swissprot;acc:p39028] 49.8325 45.2077 1.1023
SEL1L sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Subtracted Low confidence 74.9094 78.454 3.5446
SON Measured son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] High confidence 2397.19 3343.62 946.43
TAF7L Ranked tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Divided 200.791 183.66 1.09328
TBC1D5 Squared tbc1 domain family member 5. [swissprot;acc:q92609] Subtracted 30286.5 36362 6075.5
TIPRL Rooted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 66.4284 60.0004 6.428
ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Divided Low confidence 70.3674 73.7814 1.04852
383 no value Measured hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] High confidence 4533.74 5279.4 1.16447
Squared apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 15043.7 18560.1 1.23375
Rooted hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 46.1476 52.5742 6.4266
AGBL3 similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Divided Low confidence 80.2902 84.1622 1.04823
AQP1 Measured aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Subtracted 8840.39 9282.37 441.98
DCHS1 protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Divided 7115.47 7496.56 1.05356
DYNC1I1 Rooted dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted 67.1787 70.7226 3.5439
HADHA Squared trifunctional enzyme alpha subunit, mitochondrial precursor (tp-alpha) (78 kda gastrin-binding protein) [includes: long-chain enoyl-coa hydratase (ec 4.2.1.17); long chain 3-hydroxyacyl-coa dehydrogenase (ec 1.1.1.35)]. [swissprot;acc:p40939] 51199.2 47994.4 3204.8
HOXB4 Ranked homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 162.755 155.476 7.279
HRB Squared nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Divided 48780.6 45597.1 1.06982
MRPS12 Rooted 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] High confidence 49.8325 45.2077 1.1023
MXD4 Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence 205.921 198.554 1.0371
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] High confidence 237.862 217.739 1.09242
SRP9 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 4247.36 5192.61 945.25
TRUB1 Ranked trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 236.245 255.113 18.868
TULP1 Squared tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] 30286.5 36362 6075.5
384 no value Measured cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Divided 4533.74 5279.4 1.16447
Ranked small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Subtracted 227.575 208.756 18.819
Rooted 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided 50.7723 46.0607 1.10229
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Subtracted 56.185 62.6036 6.4186
ATG4C Squared cysteine endopeptidase aut-like 1; autophagin-3. [refseq;acc:nm_032852] Low confidence 49550.3 46346.5 3203.8
BLVRB flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043] Divided 44685.1 41772 1.06974
E2F1 Ranked transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] High confidence 266.421 244.236 1.09083
FBP1 Rooted fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Subtracted Low confidence 74.8883 78.4313 3.543
HARS2 Measured histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] High confidence 8061.05 9002.33 941.28
HOXC5 Ranked homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 162.755 155.476 7.279
IRX3 Measured iroquois-class homeodomain protein irx-3 (iroquois homeobox protein 3) (fragment). [swissprot;acc:p78415] Divided 8964.52 9443.02 1.05338
RAB24 Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 205.918 198.554 1.03709

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/