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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene measured description Hugo expected final
Results: HTML CSV LaTeX Showing element 451 to 500 of 3206 in total
Rank
measured
description
Hugo
expected
final
451 0.441621 XPA-BINDING PROTEIN 2 (HCNP PROTEIN) (PP3898). [SWISSPROT;Acc:Q9HCS7] XAB2 1.59982 0.27604418
452 0.215243 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 1 (EC 3.1.3.48) (PROTEIN-TYROSINE PHOSPHATASE 1B) (PTP-1B). [SWISSPROT;Acc:P18031]" no value 0.779889 0.27599184
453 0.173881 "PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2 (EC 3.1.3.48) (T- CELL PROTEIN-TYROSINE PHOSPHATASE) (TCPTP). [SWISSPROT;Acc:P17706]" PTPN2 0.6302 0.275913996
454 0.132041 TRANSDUCIN BETA-LIKE 2 PROTEIN (WS BETA-TRANSDUCIN REPEATS PROTEIN) (WS-BETATRP) (WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 13 PROTEIN). [SWISSPROT;Acc:Q9Y4P3] TBL2 0.478695 0.275835344
455 0.270501 MITOCHONDRIAL GTP BINDING PROTEIN ISOFORM V. [RefSeq;Acc:NM_032620] GTPBP3 0.981155 0.275696501
456 0.0394844 ZMAT2 0.143261 0.275611646
457 0.35534 SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNIZED BY T CELLS 1; U4/U6.U5 TRI-SNRNP-ASSOCIATED 110 KDA PROTEIN; IGE AUTOANTIGEN; SART1(259) PROTEIN; SART1(800) PROTEIN. [RefSeq;Acc:NM_005146] SART1 1.28928 0.275611194
458 2.49065 ZASP PROTEIN (FRAGMENT). [SPTREMBL;Acc:Q9Y4Z3] LDB3 9.03714 0.275601573
459 0.0421286 COLLAGEN ALPHA 3(IV) CHAIN PRECURSOR (GOODPASTURE ANTIGEN). [SWISSPROT;Acc:Q01955] COL4A3 0.15287 0.275584484
460 0.0637349 COLLAGEN ALPHA 5(IV) CHAIN PRECURSOR. [SWISSPROT;Acc:P29400] no value 0.231274 0.27558177699999997
461 0.0702636 TRANSCRIPTIONAL CO-ACTIVATOR WITH PDZ-BINDING MOTIF (TAZ). [RefSeq;Acc:NM_015472] WWTR1 0.254965 0.275581354
462 0.0869671 9 KDA PROTEIN. [SWISSPROT;Acc:P13994] CCDC130 0.315578 0.275580364
463 65 KDA YES-ASSOCIATED PROTEIN (YAP65). [SWISSPROT;Acc:P46937] YAP1
464 MITOCHONDRIAL RIBOSOMAL PROTEIN L24. [RefSeq;Acc:NM_024540] MRPL24
465 E1A BINDING PROTEIN P400; P400 SWI2/SNF2-RELATED PROTEIN; CAGH32 PROTEIN; TRINUCLEOTIDE REPEAT CONTAINING 12. [RefSeq;Acc:NM_015409] EP400
466 1.83106 LIM PROTEIN (SIMILAR TO RAT PROTEIN KINASE C-BINDING ENIGMA); ENIGMA HOMOLOG. [RefSeq;Acc:NM_006457] PDLIM5 6.64504 0.275552894
467 0.305359 "STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" SARM1 1.11055 0.274961956
468 0.0444465 GTP-BINDING PROTEIN ERA HOMOLOG (HERA) (FRAGMENT). [SWISSPROT;Acc:O75616] ERAL1 0.161679 0.274905832
469 0.218407 "TRIMETHYLLYSINE DIOXYGENASE, MITOCHONDRIAL PRECURSOR (EC 1.14.11.8) (EPSILON-TRIMETHYLLYSINE 2-OXOGLUTARATE DIOXYGENASE) (TML-ALPHA- KETOGLUTARATE DIOXYGENASE) (TML HYDROXYLASE) (TML DIOXYGENASE) (TMLD). [SWISSPROT;Acc:Q9NVH6]" TMLHE 0.794482 0.274904907
470 0.153744 "PALLIDIN; PALLID (MOUSE) HOMOLOG, PALLIDIN. [RefSeq;Acc:NM_012388]" PLDN 0.559309 0.274882042
471 1.05805 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (68KD); CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 6, 68KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR I, 68KD SUBUNIT. [RefSeq;Acc:NM_007007]" CPSF6 3.85379 0.274547913
472 0.105796 COP9 CONSTITUTIVE PHOTOMORPHOGENIC HOMOLOG SUBUNIT 3; COP9 COMPLEX SUBUNIT 3; JAB1-CONTAINING SIGNALOSOME SUBUNIT 3. [RefSeq;Acc:NM_003653] COPS3 0.385361 0.274537382
473 0.483455 HEPATOCYTE NUCLEAR FACTOR 3-GAMMA (HNF-3G) (FORKHEAD BOX PROTEIN A3) (FORK HEAD-RELATED PROTEIN FKH H3). [SWISSPROT;Acc:P55318] FOXA3 1.76198 0.274381662
474 0.454535 SEVEN IN ABSENTIA HOMOLOG 2. [RefSeq;Acc:NM_005067] SIAH2 1.65694 0.274321943
475 0.0379081 PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077] SHC2 0.138197 0.274304797
476 0.0378858 NEURONAL SHC. [RefSeq;Acc:NM_016848] SHC3 0.138116 0.274304208
477 0.126731 OVARIAN CARCINOMA IMMUNOREACTIVE ANTIGEN. [RefSeq;Acc:NM_017830] OCIAD1 0.462009 0.27430418
478 0.0444669 "SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" SLC23A1 0.162108 0.274304168
479 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] SHC1
480 0.209195 DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 7 (EC 2.7.1.-) (MAP KINASE KINASE 7) (MAPKK 7) (MAPK/ERK KINASE 7) (JNK ACTIVATING KINASE 2) (C-JUN N-TERMINAL KINASE KINASE 2) (JNK KINASE 2) (JNKK 2). [SWISSPROT;Acc:O14733] MAP2K7 0.762639 0.274304094
481 0.224714 ADP-RIBOSYLATION FACTOR 3. [SWISSPROT;Acc:P16587] ARF3 0.819215 0.274304059
482 0.0377969 "SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" SLC23A2 0.137792 0.274304023
483 0.0703022 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 (HELIX-DESTABILIZING PROTEIN) (SINGLE-STRAND BINDING PROTEIN) (HNRNP CORE PROTEIN A1). [SWISSPROT;Acc:P09651] HNRNPA1 0.256293 0.274304019
484 0.0539161 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1 (HNRNP A2 / HNRNP B1). [SWISSPROT;Acc:P22626] HNRNPA2B1 0.196556 0.274304015
485 0.0257019 CHCHD3 0.0936986 0.274303992
486 0.384939 ADP-RIBOSYLATION FACTOR 1. [SWISSPROT;Acc:P32889] ARF1 1.40333 0.274303977
487 0.0562729 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A3 (HNRNP A3) (D10S102). [SWISSPROT;Acc:P51991] HNRPA3 0.205148 0.274303917
488 0.106754 ADP-RIBOSYLATION FACTOR 4. [SWISSPROT;Acc:P18085] ARF4 0.389182 0.274303539
489 0.02648 "ZINC FINGER PROTEIN 289, ID1 REGULATED; LIKELY ORTHOLOG OF MOUSE ZFP289. [RefSeq;Acc:NM_032389]" ZNF289 0.0965355 0.274303236
490 0.0344618 CHCHD6 0.125634 0.274303135
491 ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN 3 (ARF GAP 3). [SWISSPROT;Acc:Q9NP61] ARFGAP3
492 no value
493 0.0341617 "POTASSIUM CHANNEL MODULATORY FACTOR 1; POTASSIUM CHANNEL MODULATORY FACTOR; DIFFERENTIALLY EXPRESSED IN BRANCHING TUBULOGENESIS 91; ZINC FINGER, ZZ DOMAIN CONTAINING 1. [RefSeq;Acc:NM_020122]" KCMF1 0.12454 0.274303035
494 0.277907 FUSED TOES HOMOLOG; LIKELY ORTHOLOG OF MOUSE FUSED TOES. [RefSeq;Acc:NM_022476] AKTIP 1.01314 0.274302663
495 0.309779 R3H DOMAIN PROTEIN 1. [SWISSPROT;Acc:Q15032] R3HDM1 1.12934 0.274300919
496 0.0800469 MITOCHONDRIAL RIBOSOMAL PROTEIN L18. [RefSeq;Acc:NM_014161] MRPL18 0.291858 0.274266595
497 0.25596 R3HDM2 0.9333 0.274252652
498 0.236585 no value 0.862726 0.274229593
499 0.563143 SEVEN IN ABSENTIA HOMOLOG 1. [RefSeq;Acc:NM_003031] 2.05361 0.274221006
500 0.315262 ABL-INTERACTOR 2; ABL-INTERACTING PROTEIN 1 (SH3-CONTAINING PROTEIN); ABL BINDING PROTEIN 3; ARG PROTEIN TYROSINE KINASE-BINDING PROTEIN; ABL-INTERACTOR PROTEIN 2B; SIMILAR TO SPECTRIN SH3 DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_005759] ABI2 1.14976 0.274198094

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/