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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expected Gene measured Rank final description Hugo
Results: HTML CSV LaTeX Showing element 1102 to 1151 of 3206 in total
expected
measured
Rank
final
description
Hugo
0.332147 0.0870266 797 0.262012302 ADIPOCYTE PLASMA MEMBRANE-ASSOCIATED PROTEIN (BSCV PROTEIN). [SWISSPROT;Acc:Q9HDC9] C20orf3
0.332307 0.0787698 1728 0.237039244 C12orf26
0.33238 0.0641829 2831 0.193100969 CALSYNTENIN-3 PRECURSOR. [SWISSPROT;Acc:Q9BQT9] CLSTN3
0.332615 0.0752905 2190 0.226359304 NUCLEASE SENSITIVE ELEMENT BINDING PROTEIN 1 (Y BOX BINDING PROTEIN-1) (Y-BOX TRANSCRIPTION FACTOR) (YB-1) (CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER FACTOR I SUBUNIT A) (EFI-A) (DNA-BINDING PROTEIN B) (DBPB). [SWISSPROT;Acc YBX1
0.332641 0.069842 2651 0.209962091 TUBBY RELATED PROTEIN 3 (TUBBY-LIKE PROTEIN 3). [SWISSPROT;Acc:O75386] TULP3
0.332683 0.0805704 1532 0.2421837 NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [RefSeq;Acc:NM_014062] NOB1
0.332958 0.057982 2907 0.174142084 TMEM55A
0.333333 0.0184372 3175 0.055311655 NIPA2
3176 C6orf130
3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] UBAC1
0.333672 0.0897926 602 0.26910439 ZNF703
0.334101 0.0736246 2354 0.220366296 UPSTREAM STIMULATORY FACTOR 2 (UPSTREAM TRANSCRIPTION FACTOR 2) (FOS-INTERACTING PROTEIN) (FIP) (MAJOR LATE TRANSCRIPTION FACTOR 2). [SWISSPROT;Acc:Q15853] USF2
0.335124 0.0730211 2425 0.21789278 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] XRCC3
0.335687 0.0704817 2645 0.209962554 "PROTEIN KINASE C, ZETA TYPE (EC 2.7.1.37) (NPKC-ZETA). [SWISSPROT;Acc:Q05513]" PRKCZ
0.33698 0.141847 32 0.420935961 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC (EC 2.7.1.112) (P60-SRC) (C-SRC). [SWISSPROT;Acc:P12931] no value
33 TYROSINE-PROTEIN KINASE HCK (EC 2.7.1.112) (P59-HCK/P60-HCK) (HEMOPOIETIC CELL KINASE). [SWISSPROT;Acc:P08631] HCK
0.337014 0.0906044 613 0.268844618 ZINC FINGER PROTEIN ZIC 4 (ZINC FINGER PROTEIN OF THE CEREBELLUM 4) (FRAGMENT). [SWISSPROT;Acc:Q8N9L1] ZIC4
0.337266 0.0818867 1492 0.242795598 EPIDERMAL GROWTH FACTOR RECEPTOR PRECURSOR (EC 2.7.1.112) (RECEPTOR PROTEIN-TYROSINE KINASE ERBB-1). [SWISSPROT;Acc:P00533] EGFR
0.337351 0.142003 35 0.420935465 CRK-LIKE PROTEIN. [SWISSPROT;Acc:P46109] CRKL
0.33749 0.0836052 1232 0.247726451 KIAA0859
0.337708 0.0806616 1656 0.238850131 COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q04656] ATP7A
0.337743 0.0719023 2597 0.212890571 AMYLOID BETA PRECURSOR PROTEIN-BINDING PROTEIN 1; AMYLOID PROTEIN-BINDING PROTEIN 1. [RefSeq;Acc:NM_003905] APPBP1
0.0963108 332 0.285160018 "NADH-UBIQUINONE OXIDOREDUCTASE 23 KDA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-23KD) (CI-23KD) (TYKY SUBUNIT). [SWISSPROT;Acc:O00217]" NDUFS8
0.337971 0.142264 34 0.420935524 PROTO-ONCOGENE C-CRK (P38) (ADAPTER MOLECULE CRK). [SWISSPROT;Acc:P46108] CRK
0.338193 0.0653044 2832 0.193098024 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] CLSTN2
0.338281 0.090945 614 0.26884454 DJ947L8.1.1 (NOVEL CUB AND SUSHI (SCR REPEAT) DOMAIN PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q9H4V7] no value
0.338342 0.14242 37 0.42093503 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FGR (EC 2.7.1.112) (P55-FGR) (C-FGR). [SWISSPROT;Acc:P09769] FGR
0.338961 0.14268 39 0.420933382 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE FYN (EC 2.7.1.112) (P59-FYN) (SYN) (SLK). [SWISSPROT;Acc:P06241] FYN
0.340529 0.0820308 1580 0.240892259 SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [SWISSPROT;Acc:P29508] SERPINB4
0.340556 0.0737619 2468 0.216592572 45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [SWISSPROT;Acc:Q9BRK5] SDF4
2469 "SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [SWISSPROT;Acc:Q9NRC6]" SPTBN5
2470 LSM14B
0.340942 0.143514 38 0.420933766 TYROSINE-PROTEIN KINASE ABL2 (EC 2.7.1.112) (TYROSINE KINASE ARG). [SWISSPROT;Acc:P42684] ABL2
0.341561 0.143775 36 0.42093506 PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 (EC 2.7.1.112) (P150) (C-ABL). [SWISSPROT;Acc:P00519] ABL1
0.341646 0.0836563 1366 0.244862519 "TESTIS-SPECIFIC HISTONE H2B; H2B HISTONE FAMILY, MEMBER U, (TESTIS-SPECIFIC). [RefSeq;Acc:NM_170610]" HIST1H2BA
0.34213 0.0824164 1582 0.240892059 OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [SWISSPROT;Acc:P55055] NR1H2
0.343091 0.0765571 2252 0.223139342 TRANSKETOLASE-LIKE 1 (EC 2.2.1.1) (TRANSKETOLASE 2) (TK 2) (TRANSKETOLASE RELATED PROTEIN). [SWISSPROT;Acc:P51854] TKTL1
0.343534 0.0835145 1457 0.24310403 MEGF11 PROTEIN. [RefSeq;Acc:NM_032445] MEGF11
0.343879 0.087747 986 0.255168242 HECW2
0.344638 0.0932883 568 0.270684893 SIMILAR TO KINASE SUPPRESSOR OF RAS (FRAGMENT). [SPTREMBL;Acc:Q8IVT5] KSR1
0.345038 0.0734554 2594 0.212890754 "UBIQUITIN-ACTIVATING ENZYME E1C (UBA3 HOMOLOG, YEAST); UBIQUITIN-ACTIVATING ENZYME E1C (HOMOLOGOUS TO YEAST UBA3). [RefSeq;Acc:NM_003968]" UBE1C
0.345603 0.0750119 2449 0.217046438 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] PGLS
0.346067 0.0838767 1515 0.242371275 KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 (CYTOSOLIC INHIBITOR OF NRF2). [SWISSPROT;Acc:Q14145] KEAP1
0.346879 0.144656 44 0.417021497 HEPATOCYTE NUCLEAR FACTOR 4-ALPHA (HNF-4-ALPHA) (TRANSCRIPTION FACTOR HNF-4) (TRANSCRIPTION FACTOR 14). [SWISSPROT;Acc:P41235] HNF4A
0.348604 0.0850122 1429 0.243864672 "MICROTUBULE-ASSOCIATED PROTEIN, RP/EB FAMILY, MEMBER 2; T-CELL ACTIVATION PROTEIN, EB1 FAMILY; APC-BINDING PROTEIN EB1. [RefSeq;Acc:NM_014268]" MAPRE2
0.349234 0.0826697 1745 0.236717215 GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1-LIKE 1. [RefSeq;Acc:NM_024034] GDAP1L1
0.349357 0.0424091 3018 0.121391871 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E (EC 5.2.1.8) (PPIASE E) (ROTAMASE E) (CYCLOPHILIN E) (CYCLOPHILIN 33). [SWISSPROT;Acc:Q9UNP9] PPIE
0.35015 0.083902 1618 0.239617307 ACID CERAMIDASE PRECURSOR (EC 3.5.1.23) (ACYLSPHINGOSINE DEACYLASE) (N-ACYLSPHINGOSINE AMIDOHYDROLASE) (AC) (PUTATIVE 32 KDA HEART PROTEIN) (PHP32). [SWISSPROT;Acc:Q13510] ASAH1
0.350552 0.0851899 1470 0.243016443 TRANSCRIPTION FACTOR P65 (NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT). [SWISSPROT;Acc:Q04206] RELA
0.350755 0.0849863 1529 0.242295334 KINESIN-LIKE PROTEIN KIF3C. [SWISSPROT;Acc:O14782] KIF3C

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/