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.


Navigation/Query Panel:
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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2351 to 2400 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
588 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] no value Subtracted High confidence 217.67 230.596 12.926
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] SBDS Divided 216.557 230.362 1.06375
589 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] NAV2 Low confidence 204.056 198.046 1.03035
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] PRAM1 Subtracted High confidence 217.67 230.596 12.926
ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248] RBX1 Low confidence 205.485 199.453 6.032
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] no value Divided High confidence 228.215 214.546 1.06371
590 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] AP2M1 Low confidence 211.788 218.216 1.03035
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] no value Subtracted High confidence 217.67 230.596 12.926
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] NAV2 Low confidence 204.056 198.046 6.01
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] RRM1 Divided High confidence 217.215 204.279 1.06333
591 g10 protein homolog (edg-2). [swissprot;acc:p41223] BUD31 Low confidence 201.67 195.729 1.03035
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] HRBL Subtracted High confidence 217.67 230.596 12.926
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 Low confidence 204.074 198.071 6.003
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] RPP30 Divided High confidence 216.72 230.439 1.0633
592 cda14. [refseq;acc:nm_016570] ERGIC2 Low confidence 211.525 205.3 1.03032
cgthba protein (-14 gene protein). [swissprot;acc:q12980] C16orf35 Subtracted High confidence 217.67 230.596 12.926
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] NAV3 Low confidence 204.073 198.07 6.003
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] PPP1R7 Divided High confidence 91.63 97.4011 1.06298
593 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Subtracted Low confidence 204.856 198.854 6.002
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] HTATSF1 High confidence 217.67 230.596 12.926
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] NAV1 Divided Low confidence 204.074 198.071 1.03031
tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658] DR1 High confidence 232.118 218.406 1.06278
594 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] NAV3 Low confidence 204.073 198.07 1.03031
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] CDC40 High confidence 223.282 210.136 1.06256
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] CRK Subtracted 207.26 194.346 12.914
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A Low confidence 204.843 198.851 5.992
595 ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548] ABTB1 Divided 205.485 199.453 1.03024
g10 protein homolog (edg-2). [swissprot;acc:p41223] BUD31 Subtracted 201.67 195.729 5.941
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] ABL2 High confidence 207.26 194.346 12.914
vav proto-oncogene. [swissprot;acc:p15498] VAV1 Divided 212.2 199.849 1.0618
596 doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Subtracted Low confidence 216.618 210.69 5.928
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] no value High confidence 207.26 194.346 12.914
ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248] RBX1 Divided Low confidence 205.485 199.453 1.03024
vav-3 protein. [swissprot;acc:q9ukw4] VAV3 High confidence 212.253 199.908 1.06175
597 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] ARID1B Low confidence 204.856 198.854 1.03018
probable rna-dependent helicase p72 (dead-box protein p72) (dead-box protein 17). [swissprot;acc:q92841] DDX17 Subtracted 204.837 198.913 5.924
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] HCK High confidence 207.26 194.346 12.914
vav-2 protein. [swissprot;acc:p52735] VAV2 Divided 212.526 200.212 1.0615
598 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] GRAP2 Subtracted 207.261 194.347 12.914
probable rna-dependent helicase p68 (dead-box protein p68) (dead-box protein 5). [swissprot;acc:p17844] DDX5 Low confidence 204.832 198.916 5.916
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] AKT1 Divided High confidence 248.463 234.095 1.06138
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] ARID1A Low confidence 204.843 198.851 1.03013
599 crk-like protein. [swissprot;acc:p46109] CRKL Subtracted High confidence 207.26 194.346 12.914
jumonji protein. [swissprot;acc:q92833] JARID2 Low confidence 207.726 201.813 5.913
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] AKT3 Divided High confidence 248.463 234.095 1.06138
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] SFRS3 Low confidence 208.383 202.291 1.03012
600 inhibitor of growth family, member 3. [refseq;acc:nm_019071] ING3 210.546 204.42 1.02997
neurogenin 2 (fragment). [swissprot;acc:q9h2a3] NEUROG2 Subtracted 216.554 210.642 5.912
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] ABL1 High confidence 207.26 194.346 12.914
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] AKT2 Divided 248.463 234.095 1.06138

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/